inviroranaffiat Protection Laboratory
Cincira-ati OH 45268
cr'A-ouO/8-79-006
March 1979
Research arc) Davelopment
PA Manual for
nics Analysis
Chromatography-
Mass Spectrometry
-------
RESEARCH REPORTING SERIES
Research reports of the Office of Research and Development, U.S. Environmental
Protection Agency, have been grouped into nine series. These nine broad cate-
gories were established to facilitate further development and application of en-
vironmental technology. Elimination of traditional grouping was consciously
planned to foster technology transfer and a maximum interface in related fields:
The nine series are:
1. Environmental Health Effects Research
2. Environmental Protection Technology
3. Ecological Research
4. Environmental Monitoring
5. Socioeconomic Environmental Studies
6. Scientific and Technical Assessment Reports (STAR)
7. Interagency Energy-Environment Research and Development
8. "Special" Reports
9. Miscellaneous Reports
This report has been assigned to the "SPECIAL" REPORTS series. This series is
reserved for reports targeted to meet the technical information needs of specific
user groups. The series includes problem-oriented reports, research application
reports, and executive summary documents. Examples include state-of-the-art
analyses, technology assessments, design manuals, user manuals, and reports
on the results of major research and development efforts.
This document is available to the public through the National Technical Informa-
tion Service, Springfield, Virginia 22161.
-------
TECHNICAL REPORT DATA
(Please read Inunctions on the reverse before completing)
1. REPORT NO. 2.
EPA-600/8-79-006
4. TITLE AND SUBTITLE
An EPA Manual for Organics Analysis- Using Gas
Chroma tography - Mass Spectrometry
7. AUTHOR(S)
William L. Budde and James W. Eichelberger
9. PERFORMING ORGANIZATION NAME AND ADDRESS
Environmental Monitoring and Support Laboratory
Office of Research and Development
U. S. Environmental Protection Agency
Cincinnati , Ohio 45268
12. SPONSORING AGENCY NAME AND ADDRESS ""'"'
Same as above
3. RECIPIENT'S ACCESSION-NO. _ '.
DPOQ71&4
5. RE*ORi^6Xl£ / / J. W F
March 1979 issuing date
6. PERFORMING ORGANIZATION CODE
8. PERFORMING ORGANIZATION REPORT NC
10. PROGRAM ELEMENT NO.
1BD884
11. CONTRACT/GRANT NO.
In-House Report
13. TYPE OF REPORT AND PERIOD COVERED
14. SPONSORING AGENCY CODE
EPA/600/06
15. SUPPLEMENTARY NOTES " "'' "
16. ABSTRACT
This procedural manual defines the areas of applicability of gas chromatography-
mass spectrometry in environmental analysis. The manual includes sample prepara-
tion methods specifically adapted to this measurement technique, data processing anc
interpretation methods, quality control procedures, quantitative analytical tech-
niques, utility software requirement's, preventive maintenance recommendations,
systematic trouble shooting methods, and a selected bibliography.
17. KEY WORDS AND DOCUMENT ANALYSIS
a. DESCRIPTORS
Environmental Surveys Organic
Environments Compounds
Spectroscopic Analysis
Organic Chemistry
Pollution
Ecology
Mass Spectroscopy
13. DISTRIBUTION STATEMENT '" - '
Release to Public
b. IDENTIFIERS/OPEN ENDED TERMS
.. 'i<
19. SECURITY CLASS (This Report}
Unclassified
20. SECURITY CLASS { This page I
Unclassified
c. COSATI Field/Group
1402
0703
21
22. PRICE .-'-' '-
EPA Form 2220-1 (9-73)
-------
EPA-600/ 8-79-006
March 1979
AN EPA MANUAL FOR ORGANICS ANALYSIS
USING GAS CHROMATOGRAPHY-MASS SPECTROMETRY
by
William L. Budde
and
James W. Eichelberger
Environmental Monitoring and Support Laboratory
Office of Research and Development
U.S. Environmental Protection Agency
Cincinnati, Ohio 45268
-------
DISCLAIMER
This manual has been reviewed-by the Environmental Monitoring and Support Labpratpry-
Cincinnati, U.S. Environmental Protection Agency, and apprpved for publiGatjpn. M,er»tipn pf
trade names pr cpmmercial products does not constitute endorsement or recommendation for
use.
-------
FOREWORD
Environmental measurements are required to determine the quality of ambient waters and
the character of waste effluents. The Environmental Monitoring and Support Laboratory-
Cincinnati conducts research to:
Develop and evaluate techniques to measure the presence and concentration of
physical, chemical, and radiological pollutants in water, wastewater, bottom sediments,
and solid waste.
Investigate methods for the concentration, recovery, and identification of viruses,
bacteria and other microbiological organisms in water; and to determine the responses
of aquatic organisms to water quality.
Develop and operate an Agency-wide quality assurance program to assure
standardization and quality control of systems for monitoring water and wastewater.
This publication of the Environmental Monitoring and Support Laboratory-Cincinnati
entitled: An EPA Manual For Organics Analysis Using Gas Chromatography-Mass
Spectrometry, is the result of an Agency-wide effort to document broad spectrum methods
needed for the analysis of organic compounds in environmental samples. Broad spectrum
methods are required for situations where the nature of the organic compounds that may be
present is unknown. Federal agencies, states, municipalities, universities, private laboratories,
and industry should find this manual of assistance in monitoring and controlling organic
pollution in the environment.
Dwight G. Ballinger
Director
Environmental Monitoring and
Support Laboratory-Cincinnati
-------
ABSTRACT
This procedural manual defines the areas of applicability of gas chromatography-mass
spectrometry in environmental analysis. The manual includes sample preparation methods
specifically adapted to this measurement technique, data processing and interpretation
methods, quality control procedures, quantitative analytical techniques, utility software
requirements, preventive maintenance recommendations, systematic trouble shooting methods,
and a selected bibliography.
IV
-------
TABLE OF CONTENTS
Chapter 1 Introduction ...;,... ..-. 1
Chapter 2 GC/MS Operations and Quality Assurance 4
2.1 Mass Spectrometer Start-up .., 4
2.2 Resolution and Sensitivity Adjustments , 5
DC Zero and Balance........... 5
Tune»up With Perfluorotributylamine '. 7
2.3 Data System Start-up (PPP-S) 9
Loading the Disk Operating System Bootstrap
Program 9
2.4 System Zero Adjustment 12
2.5 Mass Scale Calibration 12
Calibration Diagnostic Program 13
2.6 Quality Control '.....'........ :...' 14
2.7 Suggested Operating Parameters for Sample Analysis 18
Gas Chromatographic Considerations 18
Data Acquisition 19
Integration Time as a Function of Signal Strength
(IFSS) 21
2.8 Mass Spectrometer Shut-Down 23
Short Term 23
Long Term .;. 23
Chapter 3 GC/MS Sample Preparations 24
3.1 Water Samples 25
Direct Aqueous Injection Including Concentration
Techniques 25
Inert Gas Purging and Trapping 26
Equipment 26
Discussion ; 30
Sample Collection and Preservation 33
Procedure v 35
-------
TABLE OF CONTENTS (CONTINUED)
Qualitative Headspace Analysis 36
Extraction with -a Low Boiling Solvent 37
Reagents and Equipment K. 40
Procedure 40
Extraction with a High Boiling Solvent 42
Adsorption with Porous Polymers 43
Reagents :and Equipment 47
Procedure 47
3.2 Air Samples 48
Direct Air Injection 48
Adsorption with Porous Polymers 49
Filtration with Glass Fiber Filters 50
3.3 Sediment Samples 51
3.4 Fatty Tissue Samples 52
3.5 Chemical Derivatization Options 53
Chapter 4 Data output 55
4.1 The OUTP/CRT Software , 56
The Total Ion Current Profile 56
Cathode Ray Tube Terminal 56
Plotter 57
Mass Spectra Histograms 57
Cathode Ray Tube Terminal . 57
Plotter 58
Printed Mass Spectral Data 58
The Extracted Ion Current Profile 61
Queued Output ..62
4.2 The MSSOUT Output Software 62
The Total Ion Current Profile 64
Mass Spectra Histograms 67
Printed Mass Spectral Data 70
The Extracted Ion Current Profile '. 70
Queued Output 72
4.3 Interactive Graphics Oriented Output Software
(IGOOS) 72
Total and Extracted Ion Current Profiles 73
Mass Spectra Histograms 74
Extended Memory Output Software 75
VI
-------
TABLE OF CONTENTS (CONTINUED)
Chapter 5 Compound Identification 77
5.1 Interpretation from Theory 77
5.2 Empirical Spectrum Matching 77
Searching Printed Data Bases 77
Remote Computerized Search Systems 78
Minicomputer Search Systems 80
Procedure (PDP-8) ,; 81
5.3 Quality Control in Compound Identification 83
Evaluation of Blanks and Reagent Blanks 83
Supporting Experiments 84
Requirements for Pure Standards 88
Similarity Index Interpretations 88
The Quality Index : 88
Chapter 6 Advanced Analytical Techniques 91
6.1 Selected Ion Monitoring (SIM) 91
Definitions of Terms 92
Selection of Masses 94
SIM Using the Control Program 97
Specialized SIM Programs . 99
6.2 . Quantitative Measurements 100
Measurements with QNTSET/QNTATE 103
Measurements with QUAN3 104
Measurements with MSSOUT 105
6.3 Open Tubular Columns .. ,-. 106
Operating Variables... 106
6.4 Chemical lonization (CI) 107
Methane Chemical lonization Reference Compound 108
Principles of Chemical lonization 108
6.5 Accurate Mass Measurements 110
Chapter 7 Auxiliary Software 114
7.1 Real Time Operating System 114
Tape Initialization Programs 114
File Copy, Duplication, and Save Programs 115
File Delete and System Tape Dump Programs 116
Program to Change Machine Language Instructions 116
Program to Start the OS-8 System , 117
vu
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TABLE OF CONTENTS (CONTINUED)
7.2 The OS-8 Operating System 117
Tape Format Programs 117
Program to List Files on the OS-8 System: 118
Programs to Build Real Time Systems from Tape Dumps 118
Loading New Programs on OS-8 or the Real Time System 118
Inserting a Paper Tape Handler in OS-8 119
Loading a Paper Tape File on OS-8 119
Loading a Dectape File on OS-8 119
Loading a Binary Program on the Real Time System Disk 119
Program to Duplicate OS-8 120
Program to Start the Real Time System 120
Chapter 8 Preventive Maintenance 121
8.1 The Mass Spectrometer Vacuum System 121
Mechanical Pumps 121
Diffusion Pumps 122
Ion Gauge, Manifold, and Inlet Systems 122
8.2 The Mass Spectrometer Electronics 122
Cooling Fans and Dust Filters 122
Vacuum Tubes 123
8.3 The Gas Chromatograph ; .....;.. 123
8.4 The Data System 123
Software 123
Cooling Fans and Dust Filters 123
Lubrication of Mechanical Parts 123
Magnetic Storage Devices 124
Diagnostic Computer Programs 124
Chapter 9 Trouble Shooting 125
9.1 Mass Spectrometer Problems 125
Vacuum System 125
Ion Gauge 126
Heaters 126
9.2 Data System Problems 126
Computer Diagnostic Programs. 126
Dectape Diagnostic Programs 129
Disk Diagnostic Program 130
9.3 System Zero Adjustment Problems '. 131
vui
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TABLE OF CONTENTS (CONTINUED)
9.4 Mass Scale Calibration Problems , 131
Interface ~ Spectrometer Gain Alignment 132
Loss of Ions 132
Interface Diagnostic Programs 133
ADZERO Program 134
Peak Profile Diagnostic Program 134
9.5 Quality Control Problems 136
Poor Overall Sensitivity 136
Poor High Mass Sensitivity 136
Incorrect Mass Assignments or Poor Resolution
of Adjacent Ions 136
High Background 137
Chapter 10 Selected Bibliography , 138
10.1 General Reference Books 138
10.2 Printed Mass Spectra Collections 139
10.3 Selected Review and Primary Journal Articles 139
Mass Spectrometry 139
GC/MS 139
Direct Aqueous Injection 139
Inert Gas Purging and Trapping 139
Qualitative Headspace Analysis. 140
Adsorption with Porous Polymers 140
Air Samples '. 140
Fatty Tissue Samples 140
Chemical Derivatization 140
Selected Ion Monitoring 141
Open Tubular Columns.::., 141
Chemical lonization 141
IX
-------
LIST OF FIGURES
Figure 1.1 Flow of trace organics analysis in a laboratory with
GC/MS capability 3
Figure 2.1 Rough functional schematic showing components used in
the tune-up of a Finnigan model 1015 in the high mass range.... 6
Figure 2.2 Peaks at masses 219 and 220 10
Figure 2.3 Peaks at masses 69 and 70 10
Figure 2.4 Peaks at masses 502 and 503 10
Figure 2.5 Calibration diagnostic program plot 15
Figure 2.6 The IFSS algorithm flow chart 22
Figure 3.1 A purging device with a 5 ml sample capacity : 27
Figure 3.2 The trap assembly for a purging device 29
Figure 3.3 Recoveries of selected compounds as a function of purge
gas flow rate '. 32
Figure 3.4 Chromatogram of organohalides 34
Figure 4.1 The mass spectrum of a GC/MS reference compound,
decafluorotriphenylphosphine 59
Figure 4.2 The mass spectrum of a GC/MS reference compound,
decafluorotriphenylphosphine, with plot options 60
Figure 4.3 The extracted ion current profile for mass 149 and the
corresponding total ion current profile 63
Figure 4.4 A total ion current profile generated with
MSSOUT 65
Figure 4.5 A mass spectrum plot generated with MSSOUT 66
Figure 4.6 A mass spectrum plot generated with MSSOUT 68
-------
LIST OF FIGURES (CONTINUED)
Figure 4.7 An extracted ioircurrent profile generated with
MSSOUT 71
Figure 5.1 The extracted ion current profiles for mass 171
from a sample and the corresponding reagent blank 85
Figure 5.2 The extracted ion current profiles for mass 149
from a sample and the corresponding reagent blank 86
Figure 5.3 The total ion current profiles from a sample and the
corresponding reagent .blank..,.. '. 87
Figure 5.4 The mass spectrum of an unidentified compound and the
mass spectrum of chloropicrin 89
Figure 6.1 A schematic diagram of continuous repetitive measurement
of spectra, a TICP, and an EICP 93
Figure 6.2 A schematic diagram of continuous repetitive measurement
of spectra, SIM, and two SICP's 95
Figure 6.3 A TICP, SICP, and EICP from the chromatography of seven
chlorobiphenyl isomers..., 96
Figure 6.4 Some calculated .chlorine-bromine isotope distribution
patterns '. 98
Figure 6.5 Chemical ionization (methane) mass spectra of DFTPP as a
function of ion source temperature on the Finnigan model 4000
GC/MS system 109
Figure 6.6 Comparison of the El and CI mass spectra of
octadecane : 112
XI
-------
LIST OF TABLES
Table 2.1 Functions and corresponding potentiometer designations
for Finnigan mass spectrometers 8
Table 2.2 Octal-binary equivalents of the real time system disk
bootstrap program 11
Table 2.3 Sample report from the calibration diagnostic
program , 14
Table 2.4 Suggested GC columns and conditions 17
Table 2.5 Decafluorotriphenylphosphine key ions and ion
abundance criteria 17
Table 2.6 Representative GC columns for sample extracts 18
Table 2.7 Representative GC columns for direct aqueous
injection 19
Table 3.1 Recoveries of spiked organics from water after a simple
distillation 25
Table 3.2 Recoveries of organics by gas purging and
trapping 31
Table 3.3 Effect of residual chlorine on concentrations of
chlorinated methanes in drinking water at 4C 33
Table 3.4 Recoveries of organics by solvent extraction with
methylene chloride 38
xu
-------
LIST OF TABLES (CONTINUED)
Table 3.5
Table 5.1
Table 6.1
Table 9.1
Recoveries of organics by adsorption on porous
polymers !". 44
User options available with the mass spectral search
system '. 78
The effect of the accuracy of mass measurements and
atom constraints on the number of acceptable compositions 113
Computer diagnostic programs for the PDP-8/E
or M '.;
127
Table 9.2 Switch register selection of Dectape unit in the
random exerciser test 129
xin
-------
LIST OF PDP-8 DATA SYSTEM PROGRAMS
no file bootstrap loader 2.3
EXEC system monitor; control and IFSS prompts 2.3
INITSS .file with system configuration and constants 2.3
ZERO analog baseline adjustment 2.4
CALIBR calibrates mass scale only 2.5
FC1000 calibration driver file 2.5
M1000 calibration driver file 2.5
CDIAGN calibration diagnostics 2.5
MASDEF shifts calibration masses... 2.5
CONTRL data aquisition including IFSS 2.7
RTCON real time display on a CRT 2.7
CONDIS real time display on a CRT 2.7
CONDI1 real time display on a CRT 2.7
TWIN data acquisition on a second disk drive 2.7
EXMOD2 data acquisition on a second disk drive 2.7
PERCAL retrieves and loads operating parameters 2.7
RSTORE detailed sample information 2.7
LIST lists files on disk 0, TD8E Dectape, or
overlays MAGLST 4
LSTDSK lists files on TC08 Dectape, and disks
0,1,2, or 3 4
MAGLST list for 9 track tape 4
EXMOD1 plotter/printer dialogue .'...:.....:..:... 4.1
PLOUT plotter driver :..... .....'....... 4.1
PLOT plotter driver 4.1
PLTP2 plotter driver 4.1
CUEXEC queued plotter output 4.1
RGC generates TICP data 4.1
TYPE prints mass spectral data 4.1
BACKGD background subtract overlay 4.1
CRT main CRT program 4.1
CRTRGC overlay for CRT TICP 4.1
CRTSP overlay for CRT histogram 4.1
CBCKGD overlay for CRT background subtract 4.1
DSPLAY overlay for CRT 4.1
MSSOUT main program 4.2
MOUTP1 overlay for MSSOUT 4.2
MOUTP2 overlay for MSSOUT 4.2
MOUTP4 overlay for MSSOUT 4.2
MOUTP5 overlay for MSSOUT 4.2
MOUTP6 overlay for MSSOUT 4.2
INCCHR overlay for MSSOUT 4.2
SS1S scratch file for MSSOUT 4.2
BCLRGC main TICP/EICP program 4.3
RGCOV1 overlay for main TICP/EICP program 4.3
RGCOV2 , overlay for main TICP/EICP program 4.3
xiv
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LIST OF PDP-8 DATA SYSTEM PROGRAMS (CONTINUED)
CRTPLT main histogram plot program.;.., .-:: 4.3
PLOVL1 overlay for CRTPLT 4.3
PLOVL2 overlay for CRTPLT 4.3
SPRRGC maximized mass version of BCLRGC in 16K ; r.4.3
SPRPLT maximized mass histograms in 16K 4.3
SPRVL1 overlay for above 4.3
BRVCCP spectra abbreviation for MSSS 5.2
MDIREK transmission to MSSS-Tektronix interface 5.2
BMATCH spectra abbreviation for PDP-8 search 5.2
BMNBVT overlay for BMATCH .'...': 5.2
BMN8K PDP-8 search in 8K 5.2
BMN16K PDP-8 search in 16K 5.2
PRNTSP print spectrum in PDP-8 library 5.2
CRTSIM special SIM data acquisition : 6.1
PLTSIM special SIM data acquisition 6.1
CRSMPT special SIM output 6.1
PTSMPT special SIM output 6.1
CONVRT converts SIM datafiles to standard format 6.1
SIMEXC expanded CRTSIM in 12K 6.1
CRTSM2 overlay for above 6.2
QNTSET quantitative analysis : 6.2
QNTATE quantitative analysis 6.2
QUAN3 quantitative analysis .' 6.2
NEWTAP Dectape initialization (two versions) 7.1
NEWMAG 9 track tape initialization 7.1
COPY copies file between disk 0 or 1 and TD8E Dectape
and overlays MAGCPY 7.1
COPY copies files between disk 0 or 1 and TC08
Dectape 7.1
MAGCPY 9 track tape file copy 7.1
CPYDSK system disk duplicate 7.1
SAVE save spectra (two versions) 7.1
DELE deletes file on disk 0 or TD8E Dectape 7.1
DELE deletes file on disk 0 or TC08 Dectape 7.1
BCDELE deletes groups of files on disk 0 7.1
SYSDMP dump disk to Dectape (two versions) 7.1
MAGDMP dump disk to 9 track tape ; 7.1
PATCH change machine language instructions 7.1
OSDGO starts OS-8 system '. 7.1
DTFRMT TC08 Dectape format 7.2
TDFRMT TD8E Dectape format 7.2
PIP OS-8 file transfer and file list 7.2
TC8RES restore real time system disk from TCQ8 Dectape 7.2
TD8RES restore real time system disk from TD8E Dectape .-. -1.2
MAGRES restore real time system disk from 9 track tape 7.2
XV
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LIST OF PDP-8 DATA SYSTEM PROGRAMS (CONTINUED)
BUILD OS-8 system build , 7.2
ABSLDR OS-8 loader ..'. 7.2
FOTP 'OS-8 file transfer 7.2
LOD150 real time system loader. 7.2
DSKCPY OS-8 disk duplicate 7.2
MSDGO starts real time system from OS-8 7.2
INST1 PDP-8 instruction test 9.2
INST2 PDP-8 instruction test , 9.2
XADDR extended memory address test 9.2
XCHKBD extended core memory test 9.2
ADDER ?PDP-8 adder test , 9.2
EAEST1 EAE instruction test 9.2
EAEST2 EAE instruction test 9.2
EAEXME EAE-memory test 9.2
TC08RX TC08 Dectape exerciser 9.2
TD8DIA TD8E Dectape exerciser 9.2
DDIAGN disk format and diagnostics 9.2
MSTEST old MS 'interface test , 9.4
NEW150 new RIB interface test 9.4
ADZERO interface adjustment 9.4
MSSCAN peak profile diagnostic 9.4
XVI
-------
DATA SYSTEM RULES AND CONVENTIONS USED IN THIS MANUAL
1. Each line of response to a computer program entered from a keyboard by a user must be terminated
by pressing the return.key. This is not indicated in sample dialogue.
2. User responses in sample computer dialogue are underlined.
3. A user response to a computer program of YES may be abbreviated Y; a user response to a computer
program of NO may be abbreviated N; in most programs an N may be replaced by merely pressing the
return key. In a few programs a NO response will not be accepted and a negative input must be made by
pressing the return key. These exceptions are indicated in the sample dialogue.
4. Most user entered commands may be abbreviated with the first four characters.
5. A user may interrupt computer prompts at the keyboard \f he understands the correct response
before the output is complete. :
6. A user may usually return to the SELECT MODE: prompt by holding down the CTRL key while
pressing the L key. This is abbreviated CTRL/L frequently.
7. The compound perfluorotributylamine will be abbreviated PFTBA. This is also sometimes known by
the 3M company trade designation FC-43.
xvu
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CONTRIBUTORS
Special recognition is required for several individuals who made significant contributions to
this manual. These individuals are:
Ann Alford
Environmental Research Laboratory, EPA
Athens, GA 30601
Thomas A. Bellar
Environmental Monitoring and Support Laboratory
Cincinnati, OH 45268
Harvey W. Boyle
National Enforcement Investigation Center, EPA
Denver, CO 80225
Robert D. Kleopfer
Region VII, EPA
Kansas City, KS 66115
D. Craig Shew
Robert S. Kerr Environmental Research Laboratory, EPA
Ada, OK 74820
xvni
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ACKNOWLEDGEMENT
The authors wish to acknowledge the many others who participated in the development or
review of the manual.
Herbert J. Brass
Division of Technical Support
Office of Water Supply, EPA
Cincinnati, OH 45268
Mike Carter
Environmental Research Laboratory, :£PA
Athens, GA 30601
Emile Coleman
Health Effects Research Laboratory, EPA
Cincinnati, OH 45268
B. F. Dudenbostel
Region II, EPA
Edison, NJ 08817
Jack D. Henion
New York State College of Veterinary Medicine
Ithaca, NY 14853
Doug Kuehl
Environmental Research Laboratory, EPA
Duluth, MN 55804
Robert Lingg
Health Effects Research Laboratory, EPA
Cincinnati, OH 45268
William Loy
Region IV, EPA
Athens, GA 30601
Robert Melton
Health Effects Research Laboratory, EPA
Cincinnati, OH 45268
xix
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ACKNOWLEDGEMENT (CONTINUED)
William Middleton
Environmental Monitoring and Support Laboratory, EPA
Cincinnati, OH 45268
David J. Munch
Division of Technical Support
Office of Water Supply., EPA
Cincinnati, OH 45268
Curt Norwood
Environmental Research Laboratory, EPA
Narragansett, RI 02882
Frank Onuska
Canada Center for Inland waters,
Burlington, Ontario, Canada
James F. Ryan
Health Effects Research Laboratory, EPA
Research Triangle Park, NC 27711
Jack M. Teuschler
Environmental Monitoring and Support Laboratory, EPA
Cincinnati, OH 45268
Richard J. Thompson
Environmental Monitoring and Support Laboratory, EPA
Research Triangle Park, NC 27711
Oilman Veith
Environmental Research Laboratory, EPA
Duluth, MN 55804
Jacqueline Waitts
Bowne Time Sharing
Washington, DC 20036
Virgil L. Warren
Region VI, EPA
Houston, TX 77036
xx
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ACKNOWLEDGEMENT (CONTINUED)
Ron Webb
Environmental Research Laboratory, EPA
Athens, GA 30601
Karen Zieverink
Southwestern Ohio Regional Computer Center
Cincinnati, OH 45221
XXI
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CHAPTER 1
INTRODUCTION
The purpose of this manual is to organize in one
place a variety of information that is needed to identify
and measure organic compounds in environmental
samples using computerized gas chromatography-mass
spectrometry (GC/MS). The application of a mass
spectrometer as a universal, yet extremely selective and
sensitive detector in gas chromatography has
revolutionized the identification and measurement of
organic compounds. The efficient use of GC/MS was
made possible by the development of the relatively low
cost digital minicomputer during the late 1960's.
During the subsequent years a large number of books,
review articles, and journal articles appeared which
describe the basic concepts of the GC/MS
instrumentation, and applications to a wide variety of
organic analytical problems. A- number of these books
and articles are cited in the Bibliography in Chapter 10
of this manual. However in the environmental field the
specific detailed information that is required to utilize
this powerful tool is scattered among a variety of
sources, and some vital information is not written down
at all. The emphasis of this manual is on the
experimental details of the GC/MS methodology.
There are three distinctly different applications
where environmental measurements by GC/MS are
being or will be used widely. First, there is the broad
spectrum (BS) organics analysis which has the goal of
seeking a broad spectrum picture of whatever is present
in a sample as a major or minor component. This kind
of analysis is not guided by a predetermined list of
compounds to be measured. The BS approach was
made possible by the development of tools such as
computerized GC/MS, and this approach is
emphasized in this manual. The BS approach is most
appropriate for samples that are likely to contain
unexpected components.
Secondly, the application of GC/MS appears more
cost effective than conventional GC methods for
routine monitoring of relatively large numbers of target
compounds, e.g., 40-60 or more. Some possible reasons
for this are presented in the next paragraph. Thirdly,
the application of GC/MS in real time selected ion
monitoring is widely used in the biomedical and other
fields, and is recognized as one of the most accurate,
precise, and selective tools known to analytical
chemistry. This application requires detailed
knowledge of the compound being measured, and its
mass spectrum. This application is not emphasized in
this manual except for one section in Chapter 6.
However it is expected that selected ion monitoring
methods will become more important in the
environmental field in the future.
There are a number of contrasts between the
GC/MS methods in this manual and conventional
methods, which are often based on chromatographic
'techniques, of determining organic compounds. Both
types of methods are needed, and each has an
appropriate area of application. Conventional methods
for organic compounds are detailed chemical-
instrumental procedures designed to separate the
compound of interest (target compound, TC) from all
known interferences, and to measure its concentration
with relatively inexpensive, simple, easy-to-use
instrumentation. The separation and isolation
procedure is often called "clean-up" and is, in effect, a
large part of the qualitative analysis. The gas
chromatography-electron capture detector procedures
for chlorinated hydrocarbon pesticides are examples of
this approach. The clean-up for conventional detectors
is often quite rigorous and complex to assure that all
potential interferences are eliminated. Similarly,
because conventional methods often rely heavily on
retention indices for the identification of compounds,
rigorous control of operational conditions such as flow
rates and temperature is required. Quality control
measurements, such as retention index standards, must
be made at relatively frequent intervals to assure that
conditions are well controlled. By contrast, the
GC/MS sample preparation methods described in
Chapter 3 were designed to be as simple as possible.
1
-------
Rigorous clean-up is often not required because the
mass spectrometer output provides adequate
information, in most cases, to reliably identify the
compound. Rigorous clean-up is, of course, counter
productive in the BS approach. The GC/MS methods
do not depend on rigorous attention to operational
conditions and frequent measurements of standards for
determination of retention indices. The application of
GC/MS for routine monitoring of target compounds is
most appropriate for samples that are likely to contain
unexpected components.
Another contrast is that conventional methods
usually require a, variety of detectors to permit
measurements of a broad range of compound types.
This is because conventional detectors are designed for
some selectivity to further minimize the effects of
interfering substances. The mass spectrometer is a
universal detector which precludes interferences by the
very nature of its output. For monitoring a wide range
of compound types, it appears that the additional cost
of computerized GC/MS instrumentation may be
offset by the need to acquire and maintain only one
detector, and the use of simpler, less costly sample
preparation and quality control procedures.
Several chapters of the manual (Chapters 2,4,7,8,
and 9) describe in detail the operation and maintenance
of the Finnigan Corporation's models 1015 and 3000
series GC/MS systems with datasystems based on a
Digital Equipment Corporation model PDP-8
minicomputer. This information was included and
emphasized because the Environmental Protection
Agency (EPA) owned more than thirty Finnigan 1015
and 3000 series GC/MS systems and a similar number
of PDP-8 GC/MS datasystems. These models of
spectrometers and datasystems are in widespread use,
and the general user community should find these
specialized chapters of interest and value. Users of
other types of GC/MS systems will find information of
general interest in section 2.6, Quality Control;
Chapter 3, GC/MS Sample Preparation; Chapter 5,
Compound Identification; Chapter 6, Advanced
Analytical Techniques; and, Chapter 10, the
Bibilography.
Figure 1.1 shows a flow chart for the processing of a
sample with the BS approach. Several blocks in Figure
1.1 are identified with specific chapters in this manual.
In the BS approach, the conventional broad band GC
detector, e.g., flame ionization, may be an important
screening tool for the busy GC/MS laboratory.
Alternatively, if the current sample load is not high, the
GC/MS may itself perform the initial screening. The
GC/MS Operations and Quality Assurance Chapter
(Chapter 2) is identified with the block in Figure 1.1
labeled integer accuracy GC/MS. The importance of
reagent blanks and spectra interpretation is discussed
in Chapter 5. Chapter 6, Advanced Analytical
Techniques, includes information on methods that may
be used to obtain more information when an
identification cannot be made with integer accuracy
GC/MS. The Advanced Analytical Techniques
chapter also includes information about quantitative
measurements with GC/MS.
Contributions to and reviews of the draft chapters of
this manual were made by the participants in the EPA
mass spectrometer users group between January, 1975
and October, 1978. This users group was organized by
the authors in the spring of 1972 to promote the
exchange of technical information among EPA
laboratories using computerized GC/MS to identify
and measure organic environmental pollutants.
-------
STANDARD3-RT
CI/QC/MS
EXACT
GC-IR
YES
SAMPLE
PREPARED
FOR8C
INTEGER
ACCURACY
OC/MS
SPECTRA
INTERPRETATION
\
f
YES ,
MS OR
SIMPLE
DITECTOR
IDENTIFICATION
&
MEASUREMENT
YES
NO
3C
SIMPLE
DETECTOR
NO
*<&
Figure 1.1 Flow of trace organics analysis in a laboratory with GC/MS capability.
-------
2
GC/MS OPERATIONS AND QUALITY ASSURANCE
The purpose of this chapter is to provide the basic
information required for the successful operation of the
computerized gas chromatograph/mass spectrometer
(GC/MS). The chapter is oriented to the Finnigan
Corporation's models 1015 and 3000 series quadrupole
mass spectrometers with data systems that utilize
Digital Equipment Corporation model PDP-8
computers. However, certain portions of this chapter,
such as the quality control procedure in Section 2.6, are
readily applied to other mass spectrometer systems.
The quality control procedure is of particular
importance because one can be reasonably assured of
obtaining good quality mass spectra when the
performance criteria outlined in that section are
attained.
For initial start-up or whenever the vacuum system
is at atmospheric pressure (after changing a separator,
cleaning rods, etc.) one should follow the procedures
beginning with Section 2.1 and continue through
resolution and sensitivity adjustments, data system
start-up, system zero .adjustments, mass scale
calibration, quality control, and sample analysis.
However for normal day-to-day operation one would
begin with data system start-up followed by system
zero adjustment, mass scale calibration, and the quality
control tests. Resolution adjustments are usually
required only occasionally as indicated by the quality
control evaluation. Some suggested operating
parameters are given in Section 2.7. These parameters
should be considered as guidelines and may not
represent optimum operating conditions for every
sample which may be encountered in an environmental
analysis laboratory.
Recommended shut-down procedures for both
short-term (overnight, weekends) and long-term
situations are given. Proper shut-down procedures are
important to reduce or prevent deterioration or damage
to certain expensive components of the mass
spectrometer.
2.1 MASS SPECTROMETER
START-UP
When the vacuum system is at atmospheric pressure
(after changing a separator, cleaning rods, etc.) and the
system is completely shut down, the following
procedure is recommended for restarting the system.
1. Apply power with the vacuum controller
circuit breaker. This supplies line power to the
mass spectrometer, the gas chromatograph,
and the vacuum system.
2. Make sure that the system to be evacuated is
closed to the atmosphere (the GC end of the
separator must be capped and the direct inlet
system closed).
3. Turn on the forepump (analyzer and batch
inlet if present) switch and separator pump
switch. These switches activate the mechanical
vacuum pumps used to obtain a "rough"
. vacuum.
4. Check pressures on the forepump pressure
meter. This meter monitors the pressure down
to 0.01 torr at each forepump. If no leaks are
present, readings below 0.1 torr will be
obtained within one minute.
5. After pressures of 0.1 torr or below are
obtained, turn the vacuum controller function
switch to the override position. This turns on
the diffusion pump heaters. Since the override
position bypasses the protection circuits, the
mass spectrometer should not be left
unattended during this time.
6. After waiting approximately 45 minutes for
the diffusion pumps to heat, attempt to light
the Bayard-Alpert pressure gauge by
depressing the start button on the vacuum
controller. Depressing this button for 1-2
-------
seconds will turn on the ion gauge filament
when the system pressure is below 10"J torr. If
the filament fails to light, wait five minutes and
repeat. The life of the ion gauge filament is
shortened by high pressure operation. If the
filament stays on at 10"1 torr or greater, turn
the function switch to off, then back to the
override position and wait for lower pressure
to be obtained.
The zero control on the vacuum controller
module permits electrical zeroing of the high
vacuum meter. This can be done while the ion
gauge filament is off and the meter switch is in
the override position. Adjust the zero control
until the meter reads 1 X ICT'torr.
7. After a stable vacuum operation of 10"' torr or
lower is achieved, move the vacuum controller
function switch from override to protect.
Normally several hours are required to obtain
pressures of 10"7 torr or lower. The mass
spectrometer can be safely utilized, however,
with an analyzer vacuum of 10"' torr or less.
8. Adjust temperatures of the analyzer manifold,
transfer line, batch inlet, and interface as
desired with the heater controls on the vacuum
controller. These temperatures should be
monitored occasionally with an external
pyrometer of known accuracy. In general, the
. analyzer manifold should not be heated;- and'
the separator (interface) temperature should
be a few degrees higher than the maximum GC
column temperature to be utilized. A
temperature of about 250C is adequate for the
transfer line. The batch inlet temperature
should be sufficiently high to permit
appreciable vaporization of any liquid to be
introduced via the batch inlet (generally
100-200C).
9. Turn on the line power switch on RF/DC
power supply (1015 only).
10. Turn power on for high voltage supply to
electron multiplier (1015 only).
2.2 RESOLUTION AND SENSITIVITY
ADJUSTMENTS
Resolution and sensitivity adjustments are necessary
with a quadrupole mass spectrometer after the system
has been shut down for cleaning or replacing the
ionizer, mass filter, or the electron multiplier. They are
also necessary for other reasons such as after changing
a component on a printed circuit (PC) board in a power
supply or in the DC/RF generator. Before the mass
spectrometer resolution and sensitivity can be adjusted,
.the electronic components must be balanced. The DC
zero and balance procedure that follows was written for
the Finnigan model 1015. For the Finnigan 3000 series,
the corresponding procedure is described as a ROD
DC BALANCE ADJUSTMENT on page 1-16 of the
3000 series systems maintenance manual. Figure 2.1 is
a functional schematic of the components used in the
model 1015 tune-up.
DC ZERO AND BALANCE
1. Set the mass spectrometer as follows:
RF/DC Power Supply (bottom panel):
Line Power - On
Standby/Operate - Operate
RF/DC Generator:
Ionizer: Off
Electron Multiplier Voltage: Off
Scan Time: 0.1 sec
Scan Time Vernier: Fully clockwise
Scan Mode: Repetitive
First Mass Selector: 000
Last Mass Selector: 000
Scope Sensitivity: 0.5V./CM
2. Set the normal/test switch on the rear of the
oscilloscope to "test" position.
, '. 3. i Zero .the oscilloscope by adjusting the trace to
the center of the screen. Keep it zeroed during
the following procedure by momentarily
disconnecting the oscilloscope probe from the
test point being observed and readjusting the
trace.
4. Set the mass range selector on the model 1015
RF/DC generator to a detent position. This
removes the tuning capacitor from the RF
generator thereby curtailing the output of RF
and places PC-5 circuitry under the mid and
high mass mode of control. The mass selector
is a five position switch having one dentent
position between the high and medium range
and another between the low and medium
range.
5. Turn R-81 on PC-5 (behind the removable
panel on the RF/DC generator) fully
counterclockwise then turn clockwise 10 full
turns. This places R-81 approximately in the
center of its adjustment range when amplifier
A4 is balanced.
6. Connect the oscilloscope test probe (xlO) to
TP-3 on PC-5.
-------
-15
R81 LOW MASS COMP
R77 FINE RESOLUTION
R74 COARSE RESOLUTION
PC 5
._ _ _ _ l»r f*
(
i R179 MASS SELECT
-B-^V?A Tf (
^- R180 HIGH MASS
COMP.
-15
1.R185
~DC Z
"?-'
POS ROD
RF DRIVER
-^_ R202 BALANCE
NEG ROD
RF DR9VER
(A5)
TP4
T ,
POWER
DRIVER
946
i r j
POS ROD T
TP6
NEG ROD f
| R189
i DC ZERO
1
-(
1
r
1 .TP20
AX j, f!
R73
FEEDBACK
AJUST
RAMP
r*"- nmevEK
(A3)
1
' \
*%*»
RAWJP
FEEDBAC
(SALS)
?
RAMP
POWER
DRIVER
(Q44)
iW
~ ~ " "" PC 6
K,K C2
<*1
' ~~\
1
RF
I*" GENERATOR
807's
I-
~₯ C21=BALANCI
J^ C22=TUNE
*
' POS ROD RF
E
NEG ROD RF
L J
Figure 2.1 Rough functional schematic showing components used in the tune-up of a Finnigan model
1015inthehigh mass range.
-------
7. Turn R-185 fully clockwise until a clicking
sound is observed; then turn it counter-
clockwise until the oscilloscope trace shifts
downward about 1.5 cm (15 volts). This
balances amplifier A4 and allows R-81 to have
the maximum range of adjustment. Connect
the oscilloscope test probe to TP-4.
8. Turn R-189 clockwise; then turn it
counterclockwise until the oscilloscope display
shifts upward about 1.5 cm (15 volts). This
balances amplifier A5 (see schematic of PC-5).
The 15 volt jumps observed on the oscilloscope
are the saturation voltages of amplifiers A4
and A5. R-185 and R-189 influence the range
of R-81. If one lacks sufficient range while
adjusting the low mass resolution, R-185
and/or R-189 may not be adjusted properly.
9. Switch the mass range selector to 50-750.
10. Set first mass selector to 000 and last mass
selector to 750.
11. Connect one end of the rod balance network to
TP-5 and the other end to TP-6 on PC-5 (rod
balance network = two 100K, 1% resistors
connected in parallel to a test point).
12. Connect test probe to the junction between the
two resistors.
13. Set oscilloscope sensitivity to
20 millivolts/cm.
14. Adjust R-202 until the trace on the scope is
horizontal; then adjust R-189 until the trace is
at 0 volts. If R-189 needs to be changed more
than 2 turns, go back to R-202 and repeat
adjustment.
15. Set the normal/test switch on rear of
oscilloscope to the normal position.
After the electronic components have been balanced,
one should proceed with the resolution adjustment for
50-750 mass range.
detailed procedure is somewhat different and not
described in this manual. Potentiometer (pot)
designations (e.g., R-81) refer to'the model 1015 only.
These pot reference numbers are marked on PC-5
which is behind the removable panel of the RF/DC
generator. In parentheses after the 1015 pot number is
the pot function name. In the Finnigan 3000 series
spectrometers these names are marked on the RF/DC
controller board in the RF/DC generator. However,
the 3000 series pot numbers, which are referenced in
the manuals and on schematics, do not correspond to
the pot numbers used in the model 1015. Table 2.1
shows function names and corresponding pot
designations for the model 1015, 3000 series, and model
4000 spectrometers. Similar considerations apply to
test points.
The EPA tune-up procedure is essentially the same
as that given in Finnigan manuals except that certain
modifications are made to facilitate generating spectra
similar to that obtained with magnetic deflection
instruments. These modifications are as follows:
1. There is no optimization of signal intensity or
resolution at masses 16-18. This spectral
region is rarely, if ever, important in organic
analysis.
2. The 10% valley definition of resolution is
' -.' employed for tune-up at masses 502-503. This
improves relative signal intensity in this region
of the spectrum.
3. The magnet position, ion energy, and extractor
voltages are adjusted for maximum signal
intensity and peak shape at masses 502-503.
4. Guidelines for relative abundance criteria are
included to assist in achieving performance
consistent with magnetic deflection
spectrometers.
5. Electron energy is adjusted for optimum signal
intensity across the 50-750 amu range.
TUNE-UP WITH
PERFLUOROTRIBUTYLAMINE
The tune-up procedure that follows was written
specifically for the Finnigan model 1015 and 3000
series spectrometers. The same basic philosophy also
applies to the model 4000 spectrometer, but the
Resolution adjustment requires the introduction of
perfluorotributylamine (PFTBA) into the mass
spectrometer. PFTBA has known mass peaks and
adjacent 13C peaks up to approximately mass 600.
Significant ions are at ' the following, mass
numbers: 69-70, 131-132, 219-220, 264-265,
414-415, 502-503, and 614-615.
-------
Table 2.1. Functions and Corresponding Potentiometer Designations for Finnigan Mass Spectrometers
Function
Model
1015
Models
3000-3300
Model
4000
Low mass compensator
Coarse resolution
High mass threshold
High mass resolution
Fine resolution control
Balance for amplifier A4
Balance for amplifier A5
DC Balance
R-81
R-74
R-179
R-180
R-77
R-185
R-189
R-202
R-35
R-30
R-29
R-28
Resolution (front panel)
not applicable
not applicable
R-42
R-45
R-65
R-73
(front panel)
Using the 50-750 setting on the 1015, one is capable
of calibrating and scanning from -10 to 750 amu.
Therefore, for normal operations only the high mass
range is adjusted.
1. Set the ion source, preamp, oscilloscope, and
DC/RF generator controls as follows:
3.
system pressure at least a factor of five. If no
spectrum is observed, one may continue with
step 3, but serious problems are apparent and
trouble shooting may be required.
Turn R-179 (high mass threshold) fully
counterclockwise and R-180 (high mass
Control
Ionizer. (Filament)
lonization (Emission) Current
Electron Energy
Extractor
Ion Energy
Lens
Preamp Sensitivity
Preamp Filter
Scope Sensitivity
Electron Multiplier
Mass Range Selector
Scan Time
Scan Time Vernier
Record Switch
Scan (control) Mode
First Mass
Last Mass
Model 1015
On
0.5 milliamp
70 ev
8v
5v
- lOOv
10"' amps/v
> 3000 amu/sec
0.5 v/cm
Cu/Be, 3000v
High
0.1 sec
Fully Clockwise
Off
Repetitive
0
750
3000 Series
On
0.5 milliamp
70 ev
4v
2v
40v
10"* amps/v
> 3000 amu/sec
0.5 v/cm
Continuous dynode,
Not Applicable
GC
Not Applicable
Not Applicable
On
0
750
1600v
2. Inject 0.5 ul of PFTBA into either the batch
inlet, if you have one, or the variable leak inlet
system and admit a small amount into the
mass spectrometer. Look at scope to observe a
mass spectrum. If no spectrum is observed,
double check all settings given in step 1 and
admit additional PFTBA to increase the
resolution) fully clockwise.
Adjust the first mass and last mass controls so
that the peaks at 219 and 220 amu appear on
the oscilloscope as in Figure 2.2.
Adjust R-77 (resolution-front panel) for the
resolution between 219 and 220 as in Figure
2.2. If R-77, the fine adjustment, lacks
-------
sufficient range, set it to the middle of its
range, and adjust R-74 (coarse resolution) to
obtain roughly what is illustrated in Figure
2.2. Then go back to R-77 for the fine
adjustment. The resolution observed on the
scope is approximate and not necessarily the
actual resolution. In general, if resolution on
the scope is not quite baseline, the actual
resolution will be adequate.
6. Set the first mass and last mass controls so that
the peaks at 69 and 70 amu appear on the
oscilloscope as in Figure 2.3.
7. Adjust R-81 (low mass compensator) for the
resolution as illustrated in Figure 2.3.
Trimpots R-77 and R-81 are interactive.
Therefore steps 4 thru 7 must be repeated
several times before resolution is obtained at
both 69-70 and 219-220 amu.
8. Decrease the scope sensitivity until mass 69 is
observed completely on the scope. Adjust first
mass and last mass controls until mass 69 is on
the left side of scope and mass 219 is on right
side of scope. Mass 219 should be
approximately 35 percent as abundant as mass
69.
9. Set the first mass control so that the peak at
mass 264 is on the extreme left side of the
scope. Set the last mass control to 750.
10. Turn R-180 (high mass, resolution) fully
counterclockwise.
11. Slowly turn R-179 (high mass threshold)
clockwise until a large peak appears on the
right side of the scope. Continue turning R-179
until peak 264 on left side of scope just starts to
increase. This allows R-180 to influence
masses down to mass 264.
12. Turn R-180 clockwise until the large peak
diminishes and changes into spectral lines.
This completes a rough tune of R-180.
13. Set first mass and last mass controls to display
the masses 502 and 503. Adjust R-180 so that
resolution is as in Figure 2.4. This completes a
fine tune of R-180,
14. At this point, with peaks 502 and 503
displayed on the scope, adjust the source
magnet position, extractor voltage, and ion
energy for maximum peak height and best
peak'shape. In general the collector current
should be 70-90% of the emission current.
15. Adjust first mass and last mass controls to
display the entire PFTBA spectrum. Then
adjust the electron energy for maximum signal
intensity. The voltage observed on the meter
should then be above 50 and below 80 volts.
16. The mass spectrometer should now be ready to
calibrate. There is no advantage .to checking
resolution with the strip chart recorder.
2.3 DATA SYSTEM
START-UP (PDP-8)
This section describes in detail the start-up of a data
system based on a Digital Equipment Corporation
model PDP-8 computer. Power is applied to the
computer by turning the console key to POWER. The
POWER LOCK position also activates the system, but
the front panel is disabled and the user cannot see the
blinking lights. Peripheral devices (plotter, keyboard
terminal, etc.) may require separate activation of power
switches at some installations.
The software operating system programs are stored
on a real time system disk or on a real time system
Dectape on older systems. The disk should be inserted
into disk drive 0 (or the tape mounted on unit 1) and
the LOAD/RUN switch set to the RUN position.
About two minutes are required for the yellow
READY light to illuminate, indicating the disk is up to
speed arid ready to transfer data.
' the HALT and SING STEP switches must be up to
run a program. The operating software system is
started by running the bootstrap loader program. For
systems with a hardware bootstrap loader, the loader
program is initiated by pressing the SW switch
(adjacent to the POWER key) down, then up. If a
hardware bootstrap loader is present, the system
prompt SELECT MODE: will be displayed on the
console printer or cathode ray tube (CRT). If no
hardware bootstrap loader is included in the data
system, the loader program must be loaded manually.
The instructions for loading and running the disk
operating system bootstrap loader are in the following
section.
LOADING THE DISK OPERATING
SYSTEM BOOTSTRAP PROGRAM
The disk bootstrap program is loaded via the
computer switch register. The switch register has 12
switches, which are either up or down. A switch in the
up position represents a "1" and a switch in the down
position represents a"0". The switch register is divided
into four fields of three switches each.
-------
Figure 2.2 Peaks at masses 219 and 220.
Figure 2.3 Peaks at masses 69 and 70.
Figure 2.4 Peaks at masses 502 and 503.
10
-------
Instructions and address locations used to load the
disk bootstrap are given in four digit octal numbers to
represent the position of the 12 switches. Actual
loading procedure, however, requires that the
instructions and address locations be keyed in with
binary numbers.
The binary equivalents of the octal numbers used to
load the disk bootstrap are given in Table 2.2. Load the
disk bootstrap in the computer as follows:
1. Set the starting address, octal value 7737, in
the switch register.
2. Depress the LOAD ADDR key.
3. Set the first instruction (7200) in the switch
register.
4. Depress the DEP key.
5. Set the next instruction (6502) in the switch
register.
6. Depress the DEP key.
7. Repeat steps 5 and 6 until all instructions have
been deposited.
8. Set the computer switch register to 7737.
9. Depress the computer LOAD ADDR key.
10. Place the rotary switch in the MD position.
11. Depress the computer EXAM key.
12. Check that the first instruction, 7200, is
displayed in the computer's lower display.
13. Examine each instruction in sequence to
ensure that the bootstrap has been loaded
correctly. If a location is found to be in error,
the address of the location must first be entered
using the load address key, before the correct
instruction is entered (using the DEP key).
14. Set the switch register to 7737.
15. Depress the computer LOAD ADDR key.
16. Depress the computer CLEAR key, then the
CONTINUE.
The first message displayed by the disk operating
system is a designation of the revision level of the
software, for example, D7 or EO. The revision
described in this manual is EO. The next line displayed
is called the system prompt. It is the return point for all
programs and the user can always return to it by
holding down the CONTROL (CTRL) key while
pressing the L key on the console keyboard. A program
called EXEC and a file named INITSS are used here.
EXEC contains the system prompt, the CONTROL
and IFSS prompts, and some utility functions. INITSS
contains the system configuation information and
constants (see section 7.1).
Octal
7737
7740
7741
7742
7743
7744
7745
7746
7747
7750
7751
7752
7753
7754
7755
7756
7757
7760
Table 2.2. Octal-Binary Equivalents of the Real Time System Disk Bootstrap Program.
Address Instruction
Octal
7200
6502
6504
6512
1356
6517
7200
6514
6501
5347
6511
5760
6505
7402
5337
7757
1400
0400
Binary
1 1 1
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
111
Oil
100
100
100
100
100
100
100
100
101
101
101
101
101
101
101
101
110
111
000
001
010
on
100
101
110
111
000
001
010
on
100
101
no
111
000
111
110
110
110
001
110
111
110
110
101
no
101
no
in
101
in -
001
000
Binary
.010 000
101
101
101
on
101
010
101
101
on
101
111
101
100
on
in
100
100
000
000
001
101
001
000
001
000
100
001
no
000
000
on
101
000
000
000
010
100
010
no
in
000
100
001
in
001
000
101
010
111
111
000
000
11
-------
2.4 SYSTEM ZERO ADJUSTMENT
This adjustment is extremely important and should
be checked frequently, at least once each work day. The
zero adjustment defines an electronic threshold or
baseline for the acquisition of mass spectrometric data.
Any signal from the mass spectrometer that is below
the threshold will not be observed by the data system.
All signals that are above the threshold will be
measured. If the threshold is too high, small but real
signals will not be observed. This reduced sensitivity
will be accompanied by inaccuracies in ion abundance
ratios. If the threshold is too low, there will be a
decrease in the signal/noise ratio and the mass spectra
will contain many 2-5% relative abundance signals
that are meaningless.
The zero adjustment is accomplished under
computer control by running the zero program. The
program is called by responding ZERO to the system
prompt:
SELECT MODE: ZERO
MANUAL?: N_
AUTOMATIC?: N_
ZERO ADJUST?: Y_
The MANUAL prompt is used to maintain or release
computer control of the mass spectrometer. A Y_
response causes the computer to release control of the
spectrometer, that is, put it in the manual mode, and
the data system will return to the system prompt.
Therefore to use the zero program the user must
respond to MANUAL with an N. The AUTOMATIC
prompt was intended for a future implementation of an
automatic zero adjust. This has not been accomplished
yet, and the user should respond N. After a Yjesponse
to the ZERO ADJUST?, the data system monitors the
output of the mass spectrometer at a particular mass.
In earlier versions of the software, for example D2, the
zero program monitored a mass at the very low end of
the mass scale in the 10 * 30 amu range. In later
versions, for example D5, this was changed to monitor
a mass in the 450 - 500 amu range. The user should
make certain that the later version of the zero program
is used for the zero adjustment. In the lower mass range
there is often significant background from air
components and other common gases. If the zero
program is run with the ion source and electron
multiplier turned on, as is recommended, this
background will cause the threshold to be set too high.
In the range of 450 - 500 amu there is very little
natural background and a better zero adjustment may
be accomplished.
The actual threshold adjustment is made, while the
zero program is running, by turning the preamplifier
zero adjust control' until just one light (octal 0001) is
observed flashing on and off in the computer
accumulator. Zeroing should be performed with the
preamplifier switch in the position to be used during
data acquisition. The rotary switch on the PDP-8 front
panel must be set to the AC position to display the
contents of the accumulator in the front panel lights. If
no accumulator lights are displayed, the threshold is
too high; if more than one accumulator light is
displayed, the threshold is too low.
As previously indicated, the zeroing operation
should normally be performed with the ionizer and
electron multiplier power applied. This should correct
for background noise which exists while the mass
spectrometer is acquiring data. Many Finnigan
GC/MS operators prefer to zero with no power applied
to the ionizer and electron multiplier. In theory, if the
ionizer is reasonably clean and the electron multiplier is
not noisy, the zero setting, with 0001 showing in the
accumulator, should be approximately the same with
ionizer and power supply on or off. Background noise,
however, often affects the preamplifier zero value.
After the attainment of a satisfactory zero, the
CTRL/L key is used to return to the system prompt. If
a stable zero adjust cannot be achieved, there is a
serious hardware problem and the trouble shooting
chapter should be consulted.
2.5 MASS SCALE CALIBRATION
The calibration of the mass scale should be checked
at the beginning of each day. See section 2.6. If
calibration is required the program CALIBR is used
for this purpose. Mass scale calibration, requiring
approximately 40 seconds, is accomplished over the
mass range or over a superset of the mass range selected
for spectrum acquisition. The mass scale calibration
compound perfluorotributylamine (PFTBA) is injected
into the mass spectrometer, and the system
automatically calibrates the mass scale using ions from
this compound. A file with the calibration data (mass
numbers relative to mass set voltages) is automatically
created. It should be noted that this procedure does not
calibrate ion abundances. *..
12
-------
To calibrate, the operator calls the calibration
program:
SELECT MODE: CONTROL OR IFSS
CALIBRATE?: Y_ .
CALIBRATION FILE NAME: UP TO SIX
CHARACTERS
MASS RANGE: 20-700
MS RANGE SETTING?: H_
NON STND CAL?: N^
DO CALIB DIAGNOSTIC?: Y_ OR N_
The calibration program uses the IFSS mode which
is explained in Section 2.7. However, it may be called '
by responding to the system prompt with CONT or
IFSS
The calibration file name defines the file which will
contain the current calibration data. The file name is
used in each data acquisition run to define the mass set
voltages to be applied by the data acquisition routine. If
the calibration file name entered already exists in the
directory, the calibration routine is aborted, an error
message is displayed, and the system returns to the
system prompt.
The MASS RANGE prompt specifies the range of
mass units covered by the calibration file. Only one
mass range may be selected for calibration, it must
include masses 69 and 100, and the first and last.masses
must be separated by a hyphen.
The MS RANGE SETTING? prompt refers to a
mass range switch on the model 1015 and earlier
spectrometers. The user responds to this inquiry with
an H, M. L, or P corresponding to the mass range
selected on the mass spectrometer electronics console.
H, M, L, and P refer, respectively, to the high-mass
range (50-750), mid-mass range (10-250), low-mass
range (1-100), and peak identifier mass range (1-500).
The 3000 series systems have a single mass range and
the user responds with an H. It is recommended that
1015 and earlier model users calibrate the high mass
range for most general purpose work.
The NON STND CAL? prompt is used for
calibration with PFTBA on instruments with an
extended mass range (> 750 amu) or for calibrations
with any alternative mass calibration compound. For
calibrations up to 750 amu of extended mass range
instruments with PFTBA, the user responds Y.
Another prompt requests the name of the overlay file
and the correct response is FC1QOO. A separate overlay
file is, required for each alternative mass calibration
compound. For example, with tris (per-
fluoroheptyl) triazine as the mass scale calibrant, the
overlay filename is M1000. The user should be aware
that calibration to 1000 amu requires a change in a
system status word as described in section 7.1 For
calibrations of instruments with a mass range to
750 amu, the response is N_
For the first calibration the user must respond N_to
the DO CALIB DIAGNOSTIC? prompt. Once the
system has been calibrated, and assuming the
calibration file was not deleted, the calibration
diagnostic feature may be used. After the response to
this prompt is entered, the operator must be sure the
ionizer is on, and the pressure of PFTBA is adequate
for calibration. When calibration is completed, the
operating system returns to the system prompt.
A program called MASDEF may be used to shift
calibration masses by a constant amount per 100 amu
to correct for fractional masses. The program operates
on existing calibration files, and the user has several
choices of mass shifts. For example, if a shift of +0.06
amu is selected (one of several possibilities), the
program sets up a continuous shift of 0.06 amu at 100
amu, 0.09 at 150 amu, 0.13 at 220 amu, etc. Thus one
may use a standard PFTBA calibration file and correct
for large fractional masses in saturated aliphatic
hydrocarbons while using the higher scan speed
availabe with one sample/amu. Negative shifts are also
available and have several potential applications.
CALIBRATION DIAGNOSTIC PROGRAM
An affirmative response to the DO CALIB
DIAGNOSTIC? prompt calls the program CDIAGN
and leads to another prompt:
SELECT MODE: CONTROL OR IFSS
CALIBRATE?: Y_
CALIBRATION FILE NAME: UP TO SIX
CHARACTERS
MASS RANGE: 33-700
MS RANGE SETTING?: H_
NON STND CAL?: N[
DO CALIB DIAGNOSTIC?: Y_
PREV CALIB FILE NAME: UP TO SIX
CHARACTERS
After input of the name of the previous calibration
filename, which still exists on the disk, the program
produces a report on the console printer or CRT. A
sample report is shown in Table 2.3.
The first row of the report gives the amplitudes
(AMP) of the peaks that were used in the current
calibration. The mass numbers (AMU) that correspond
to these amplitudes are shown in the bottom row. The
13
-------
second row, labeled DEL N (delta N), shows the
respective changes in digital-to-analog converter
(DAC) values from the previous calibration file. This is
perhaps the most significant set of data in the report.
Generally when calibration files are compared, and
there has been very Irttle drift since the previous
calibration, the DEL N values will be no greater than
5-8. If several days have elapsed between calibrations,
DEL N values can be expected to approach 10-20 with
the Finnigan 1015. DEL N's significantly greater than
these values indicate a drifting mass spectrometer or,
less likely, a data system problem. The next row of
values labeled T, MS is the time, in milliseconds, over
which each ion signal was integrated. The amplitude
value must be divided by the integration time at each
mass to calculate comparable ion abundance values.
The row of values labeled N is the DAC value, in octal,
that was supplied to generate the mass set voltage for
each mass in the current calibration file. To reiterate,
the key value is the drift in DAC value of a given mass
between calibrations (DEL N).
require valid mass spectra of the compounds detected.
This is independent of the actual method of
interpretation of the spectra, i.e., -an empirical search
for a match within a collection of authentic spectra or
an analysis from the principles of organic ion
fragmentation. A properly operating and well tuned
GC/MS is required to obtain valid mass spectra.
The purpose of the quality control test is to make a
quick check - about 15 minutes - of the performance
of the total operating system of a computerized
GC/MS. Thus with a minimum expenditure of time, an
operator can be reasonably sure that the GC column,
the enrichment device, the ion source, the ion
separating device, the ion detection device, the signal
amplifying circuits, the analog to digital converter, the
data reduction system, and the data output system are
all functioning properly.
An unsuccessful test requires, of course, the
examination of the individual subsystems and
correction of the faulty component. Environmental
data acquired after a successful systems check are, in a
Table 2.3. Sample Report from the Calibration Diagnostic Program.
MONITOR REPORT:
AMP
DEL N
T, MS
N
AMU
0
0
0
1465
20
234
0
1
2207
28
93
0
16
4053
50
726
-2
1
5522
69
70
-1 .
1
10173
100
244
-1
1
12646
131
71
-1
4
15774
169
233
0
1
22130
219
89
0
8
42363
414
107
1
. 64
63163
614
PLOTTER READY?
An affirmative response to the PLOTTER READY
question in the Monitor Report will produce the plot
shown in Figure 2.5. The diagnostic program uses the
table of mass set voltage values that the calibration
program generated, scans over the ions that were used
in the current calibration, and plots the peaks. This plot
provides the user with the peak shapes to determine
whether resolution was adequate. From these shapes,
the user can also determine the condition of the ionizer.
Very heavily skewed peaks often indicate that cleaning
is required. The plot also gives the operator a record of
calibration data on a day-to-day basis. The plot shows
relative abundances, the masses of the ions used in
calibration, the DAC value settings for each mass, and
the integration time spent on each ion. It also allows the
user to label the conditions used in calibration that day.
2.6 QUALITY CONTROL
Correct identifications of organic pollutants from gas
chromatography mass spectrometry (GC/MS) data
real sense, validated and of far more value than
unvalidated data. Environmental data acquired after an
unsuccessful test may be worthless and may cause
erroneous identifications.
It is recommended that the test be applied at the
beginning of a work day on which the system will be
used and also anytime there is a suspicion of a non-
obvious malfunction.
The test was written specifically for the Finnigan
quadrupole mass spectrometer equipped with a Digital
Equipment Corporation Model PDP-8 computer.
However, the test is clearly and readily adapted to any
GC/MS system by suitable modification of the detailed
procedure. Indeed data from other GC/MS systems
was used to establish the abundance criteria of the test
(Analytical Chemistry, £7,995, 1975).
There is a special need to closely monitor the
performance of the quadrupole mass spectrometer.
Unlike the magnetic deflection spectrometer, the active
ion separating device of the quadrupole spectrometer,
the rods, is directly contaminated during operation and
14
-------
B 1 I u II I i/ft>»v J
, A. L
^ yi\, ,
*, i/lW i/JVji iAj iAjL i 1
Mi 20 I 28 I SO 1 69 1 108 1 131 I 169 1 219 1 261 I 111 I 332 I 611 I 650 I
N 1312 17S2 3102 1661 7031 11201 137S3 17111 22S67 3S3H 13577 S3S11 5S2B1
T 0 1 16 1 1 1 1 1 1 1 1 61 0
-------
after prolonged operation is subject to severely
degraded performance. Since degraded performance
usually affects the high mass region first, the test
includes the high mass end criteria. High quality high
mass data is important since many environmentally
significant compounds 'have molecular and fragment
ions in the 300-500 amu range.
A quadrupole spectrometer which meets the criteria
of this test will, in general, generate mass spectra of
organic compounds which are very similar, if not
identical, to spectra generated by other types of
spectrometers. Thus quadrupole mass spectra will be
directly comparable to spectra in collections which
have been developed over the years with other types of
spectrometers.
The reference compound used in this test is available
from PCR, Inc., P. 0. Box 1778, Gainesville, Florida
32602.
Procedure:
3.
4.
Make up a stock solution of
decafiuorotriphenylphosphine (DFTPP) at 1
milligram/milliliter (1000 ppm) concentration
in acetone (or a hydrocarbon solvent). This
stock solution was shown to be 97 + % stable
after 6 months and indications are that it will
remain usable for several years. Dilute an
aliquot of the stock solution to 10
microgram/milliliter (10 ppm) concentration
in acetone. The very small quantity of material
present in very dilute solutions is subject to
depreciation due to adsorption on the walls of
the glass container, reaction with trace
impurities in acetone, etc. Therefore this
solution may be usable only in the short term,
perhaps one week.
Adjust the flow from the GC column to 30
cc/min at the exit, attach the column to the
spectrometer, and set desired oven
temperature. Some suggested GC columns and
conditions are listed in Table 2.4. Parameters
should be adjusted to permit at least four mass
scans during elution of the DFTPP. This will
permit selection of a spectrum that is
reasonably free of abundance distortions due
to rapidly changing sample concentration.
Set sensitivity to 10'7 and zero instrument
using the automatic ZERO program.
Set up the real time system for control mode
with the following variables: (see section 2.7
for additional information).
SELECT MODE: CONT
CALIBRATE?: N_
TITLE: DFTPP + THE DATE
CALIBRATION FILE NAME: CAL
FILE NAME: UP TO SIX CHARACTERS
MASS RANGE: 40-450
INTEGRATION TIME: 8_
SAMPLES/AMU: j_
THRESHOLD: press return
RT GC ATTEN: 5_
FAST SCAN OPT?: press return
MS RANGE SETTING?: H_
MAX RUN TIME: 20
DELAY BETWEEN SCANS (SECS.)?:
press return
5. Inject 20 ng (2 ul) of the dilute standard into
the GC column.
6. After the acetone elutes from the column and
is pumped or diverted from the system, turn on
the ionizer and start scanning.
7. Notethe exact retention time of the DFTPP as
it elutes from the column as indicated on the
realtime GC. This retention time can be used
as a daily check of the condition of your GC
column and separator by comparing the
values. The retention times should not vary
significantly from day to day with identical
operating conditions.
8. Terminate the run by pressing CTRL/L, turn
the ionizer and multiplier off, and plot the total
ion current profile (see chapter 4.)
9. Select a spectrum number on the front side of
the GC peak as near the apex as possible and
select a background spectrum number
immediately preceding the peak.
10. The mass spectrum can be output in various
ways including a plot of the full spectrum on
the plotter or cathode ray tube or a print of the
full spectrum on a printer or cathode ray tube
(see chapter 4). A print of a partial spectrum
using the following responses is usually
convenient:
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N^
EXTRACTED ION CURRENT PROFILE?: N^
PLOT SPECTRUM?: N_
PRINT SPECTRUM?: Y_
FILE NAME: YOUR FILENAME
SPECTRUM NUMBER.: APPROPRIATE
SPECTRUM NUMBER
16
-------
PARTITIONED OUTPUT?: Y_
MASS RANGE: 51;68-70;127;197-199;
275:365:441-443
MINIMUM VALUE %: press return
SUBTRACT BACKGROUND: Y_
SPECTRUM NUMBER: APPROPRIATE
SPECTRUM NUMBER
BACKGROUND AMPLIFICATION:
press return
SAVE SUBTRACTED FILE?: N_
NORMALIZE ON: press return
ions in Table 2.5. Figure 4.1 is a plot of an acceptable
DFTPP spectrum.
If the relative abundances are not within the limits
specified, the appropriate adjustments should be made
using the proper trimpots on PC-5 of the Finnigan
1015: R-81 (low mass compensator) for the low mass
range, R-77 (resolution, front panel) for the medium
mass range, and R-180 (high mass resolution) for the
high mass range. The magnet position and ion energy
may need to be adjusted very slightly to cancel out
front end liftoff. When an acceptable spectrum is
Table 2.4. Suggested GC Columns and Conditions1
Dimension (Type)
6' x 2 mm ID
(Glass)
6' x 2 mm ID
(Glass)
6' x 2 mm ID
(Glass)
6' x' 2 mm ID
(Glass)
1.95% QF-1 plus
1.5% OV-17 on
80/100 mesh Gas-Chrom Q
3% OV-1 on 80/100
mesh Chromosorb W
5% OV-17 on 80/100
mesh Chromosorb W
1% SP2250 on 100/120
mesh Supelcoport
Flow Rate
30 ml/min
30 ml/min
30 ml/min
30 ml/min
220
220
170
R. Time
4 min.
5 min.
5 min.
5 min.
'Use any column of your choice which gives at least four mass scans during elution of the DFTPP.
obtained, it should be recorded for permanent storage.
Table 2.5. Decafluorotriphenylphosphine Key Ions and Ion Abundance Criteria.
The spectrum obtained on the test system should
contain ion abundances within limits given for the key
Mass Ion Abundance Criteria
51 30-60% of Mass 198
68 Less than 2% of Mass 69
70 Less than 2% of Mass 69
127 40-60% of Mass 198
197 Less than 1% of Mass 198
198 Base Peak, 100% Relative Abundance
199 5-9% of Mass 198
275 10-30% of Mass 198
365 At least 1% of Mass 198
441 Less than- Mass 443
442 Greater than 40% of Mass 198
443 17-23% of Mass 442
17
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2.7 SUGGESTED OPERATING PARA-
METERS FOR SAMPLE ANALYSIS
This section deals with the instrumental portion of
the analysis after the sample or sample extract has been
properly prepared. Details concerning sample
preparation are given in Chapter 3. The first part of this
section deals with aspects of the gas chromatography
itself and includes a list of some recommended
columns. The second part describes the operating
parameters required for data acquisition.
GAS CHROMATOGRAPHIC
CONSIDERATIONS
In order to achieve optimum separations, the
selection of the column and gas chromatography
operating conditions are of utmost importance.
Certainly the degree of separation of components in a
complex mixture has a direct bearing on the ability to
make unambiquous mass spectral identifications.
Publications dealing with selection of the liquid phase
and the solid support, along with other operating
parameters are referenced in the bibliography (Chapter
10).
Generally, 6 ft. X 1/4 in. O.D.-(.08 in. I.D.) packed
glass columns with helium carrier gas flowing at 20-30
ml/mm are utilized for environmental samples.
Comments on open tubular columns are in section 6.3.
Silanized glass wool plugs and silanized solid supports
of 80/100 mesh are recommended. While using the
GC/MS system, one must be alert for the occurrence of
leaks or a plugged separator. Normally with helium
flowing through the column at 20-30 ml/min, the
separator forepump pressure will be 0.1 torr or higher.
A pressure lower than this indicates either, a leak
upstream from the separator or a plugged separator.
The normal high vacuum pressure is 10"5 to 10"* torr
with helium flowing through the separator. A pressure
of 10"* torr or lower indicates a plugged separator.
Injections of methylene chloride or chloroform
solutions should be avoided on systems without a
diverter valve because injections of more than two
microliters may cause an excessive increase in pressure
in the mass spectrometer which may automatically
shut down the system. Acetone and hexane are
acceptable solvents to use. Injections should be made
with the ionizer off. The elution of the solvent from the
column is indicated by a deflection of the high vacuum
pressure gauge. After the pressure has returned to
normal the ionizer may be turned on and data
acquisition can be initiated. However, for systems with
a diverter valve, appropriate measures should be taken
to divert the solvent from the mass spectrometer.
Under these conditions .large injections of even
troublesome solvents may be quite possible. With
hexadecane or tetralin extracts (extraction with high-
boiling solvents for determination of volatile
components) data acquisition should be started prior to
injection and stopped just before elution of the solvent.
Some representative columns for separation of
environmental extracts are listed in Table 2.6. Only
well conditioned columns should be used and the
maximum operating temperatures should never be
exceeded.
Table 2.6. Representative GC Columns for
Sample Extracts.
Column
Maximum Operating
Temperature
1.5% OV-17 + 1.95%
QF-1 on Supelcoport
5% OV-17 on
Gas-Chrom Q
3% OV-101 on
Gas-Chrom Q
4% FFAP on
Gas-Chrom Q
3% Dexsil 300 on
Chromosorb G 60/80
1% SP2250 on 100/120
Mesh Supelcoport
250C
300C
300C
200C
400C
375C
Certain compounds can be determined by direct
aqueous injection into the gas chromatograph. The
ionizer is turned on and data collection is initiated
immediately after elution of the water. Some
representative columns for aqueous injections are listed
in Table 2.7.
18
-------
Table 2.7. Representative GC Columns for Direct
Aqueous Injection.
Column Packine
Chromosorb 101
80/100 mesh
4% FFAP on
Chromosorb W
60/80 mesh
Application
General for Low Molecular
Weight Compounds up to
MW 200. Water elutes
before organics
Phenols, Acids
0.4% Carbowax 1500 Low Molecular Weight
on Carbopack A
Tenax GC 60/80
mesh
Carbowax 400 on
Porasil C 100/200
mesh
Acids
Amines
General for Low
Molecular Weight
Compounds
DATA ACQUISITION
There are two data acquisition modes available to
real time system users. The CONTROL mode utilizes a
fixed integration time for each mass that is monitored
while in the IFSS mode the integration time is varied as
a function of the signal strength. The principal file that
must be present on the disk is named CONTRL. This
handles data acquisition for the CONTROL and IFSS
modes. For real time display on the CRT the files
RTCON and CONDIS must be present. For data
acquisition and storage of accurate time data with the
remote in base (RIB) interface, the file CONDI 1 must
be present. For data acquisition on a second disk drive
the files TWIN and EXMOD2 must be present. None
of these files are directly called by the user
As shown in the examples in Section 2.6 and Chapter
3, data acquisition is initiated by answering
CONTROL to the system prompt followed by a NO
response to the calibrate question-. The operator then
enters the required information for each of the
remaining prompts which are described as follows:
TITLE: The title, which is later printed or plotted on
the data outputs, can include up to 64 characters which
identify and describe the samples. Such things as
sample number, date, and gas chromatographic
conditions may be included here.
CALIBRATION FILE NAME: The calibration file
. name is the file which contains the current calibration
data (see Section 2.5 for details on calibration).
FILE NAME: This input, which may be up to six
characters in length, identifies the data acquisition file.
This file name is used later to output data.
MASS RANGE: This input specifies the atomic mass
units which are to be scanned during data acquisition.
One can have a single mass range, a set of up to 8 mass
ranges, or, up to 8 individual atomic mass units. The
mass range inputs must be entered in ascending
nonoverlapping order separated by semicolons. The
mass range inputs need not be contiguous.
Prior to initiating data acquisition, the control
routine checks the operator inputs against the inputs
specified for the calibration file. This check ensures that
the mass range is a subset of the values specified in the
calibration file. If there is a discrepancy in the mass
range setting, (see below) or if the user attempts to run
outside of the calibration file range, the run will be
aborted, and an error message will be printed on the
console or CRT.
INTEGRATION TIME: This input specifies the
time in milliseconds over which the mass spectrometer
monitors each individual mass. A numeric value of 1 to
4095 is entered for each mass or mass range entry.
These are separated by semicolons.
SAMPLES/AMU: This parameter can be used to
compensate for noninteger masses (for example, 243.2)
when necessary. The number of samples to be taken per
atomic mass unit must be in the range of 1 to 10.
Normally an input of one is used. This provides
sampling at integer mass units only. However, a larger
number can be utilized in which the data acquisition
program proceeds from the integer amu by 0.1 amu
steps until the number of samples per amu has been
exhausted. The highest intensity point is then recorded
as the peak center. A single numeric value defining the
number of samples/amu must be entered for each mass
range selected. For example, an entry of 1;4;1 coupled
with a mass range entry of 40-100; 101; 102-190 would
result in sampling at integer mass units for each mass
except 101. Mass 101 would be sampled at 101.0, 101.1,
101.2, and 101.3.
THRESHOLD: This input is a single numeric value
which applies to the entire mass range being monitored.
The number, which represents an integer multiple of
.025% of full scale, defines the background noise
threshold of the system. The data acquisition software
uses this value "as the lower'limit for the retention of
data. A sample point whose ion intensity does not
19
-------
exceed this limit is discarded and reported as zero
intensity. The input range is from 0 to 4095 and the
default value is 0. This value modifies the zero setting
described in Section 2.4, and should be used with
caution.
RT ON CRT?: A negative response to this causes the
program to put the real time gas chromatogram on the
plotter, and even if the remote in base (RIB) interface is
present, no real time clock data is saved. An entry of Y
or YG initializes the real time clock capability if the
system has a RIB interface. A Y causes display on the
CRT of every third mass spectrum if the integration
time is 3 msec or longer; if the integration time is less
than 3 msec, the program bombs! A YG causes display
of the total ion current profile (TICP) on the CRT. Far
more important, when the DATA prompt is printed
and the user presses the space bar, the real time clock is
zeroed and started. The CRT or TTY bell will ring
every two seconds; when the user presses RETURN,
data acquisition begins. Thus the clock may be started
at injection time and data acquisition started
subsequently. Alternatively pressing RETURN
immediately after the DATA prompt zeros and starts
the clock and data acquisition. The real time clock data
is saved with the data file, and the MSSOUT software
only (Chapter 4) may be used to output a
chromatogram with the X axis in spectrum numbers or
time in minutes.
RT GC ATTEN: This is a value from 1 to 8 which
attenuates the real time output of the total ion current
profile recorded on the digital plotter. The default
value is 1. For displays on the CRT, the attenuation of
the spectrum is accomplished with switch registers 0-5;
the attenuation of the TICP is accomplished with
switch registers 6-11. The switch registers may be
changed during the course of the run, and on both the
larger the octal number the more the attenuation of the
display.
FAST SCAN OPTION?: This option modifies the
overall scan rate of the system, by reducing the settling
time (ordinarily 2.3 milliseconds) between successive
mass peaks. A response of yes should be made only if
this hardware option has been installed.
MS RANGE SETTING: This indicates the range to
be used (High, Medium, or Low) during data
acquisition with a model 1015. The operator responds
with an H, M, or L, depending on the mass range
selected on the mass spectrometer electronics console.
Npte that the calibration file utilized must also
correspond 'to the mass range setting. This was
described more completely in Section 2.5. The 3000
series users should respond with an H
MAX RUN TIME: This specifies, in minutes, the
duration of data acquisition. A response of zero or
pressing the return key. results in only one scan being
made. The upper limit for this entry is 2047 minutes.
DELAY BETWEEN SCANS (SECS.): An input
here allows one to delay between scans from one second
to 2047 seconds. No response results in no delay
between scans.
SECOND DISK?: When data acquisition on a second
disk (Dl) is carried1 out, the current calibration file
must be present on the second disk. The file name
created on Dl is exactly the same as the designated file
name on DO, and the file on Dl starts over at spectrum
number 1. The response to this prompt is YES or NO,
depending on whether data acquisition should be
continued on the second disk if the first disk becomes
filled to capacity.
After all of the prompts have been answered, the
computer responds with DATA and acquisition begins
when the return key is depressed. Data acquisition will
end when the previously stipulated maximum run time
is reached or it can be halted manually by
simultaneously depressing the CONTROL and L keys.
The time required to scan a complete mass spectrum
can be determined from the mass range, the integration
time, the number of sample/amu, and the settling time
which is normally 2.3 milliseconds. For example, data
acquisition in the control mode with a mass range of
40-400, one sample/amu, and an integration time of
8 ms would result in scan times of 3.7
seconds: (400-40) X (8 + 2.3) = 3708 ms.
Generally scan times of 3-5 seconds are adequate to
produce good quality mass spectra. However, shorter
scan times may be necessary for early eluting narrow
GC peaks. The scan time must be multiplied by the
number of sample/amu, and this could increase scan
time significantly.
The same operating parameters may be used for data
acquisition at a later time because these parameter
values are stored with the data file. Reuse of the same
parameters requires that the data file be present on the
disk. The program used to implement this capability is
called PERCAL. The name of an existing data file is
entered and PERCAL retrieves the stored operating
parameters, e.g., mass range, samples/AMU, etc. and
prints them on the CRT or TTY; also PERCAL places
them in their proper places in core memory for use in
the next data acquisition.
SELECT MODE: PERCAL
FILE NAME?: TEST
TYPE OF RUN: CONTROL
20
-------
RUN TITLE: DEMO
CAL FILE NAME: CAL
NB. OF RANGES: 0001
MASS RANGES: 0035-0500
INTEG.TIME(S): 0008
SAMPLE/AMU: 0001
THRESHOLD: 0000
MAX. RUN TIME: 0025M
DL BET. SCANS: OOOOS
RT GC ATTEN: 0003
NB. OF SPECTRA: 0485
NB. OF POINTS: 0000
FILE NAME?:
Entry of another file name will cause the program to
access another datafile and repeat the process. Entry of
CTRL/L causes a return to SELECT MODE, but with
the data from the latest PERCAL saved in core. If the
response to SELECT MODE is an asterisk, a new data
acquisition may begin svith minimum dialogue using
the same operating parameters.
SELECT MODE:
FILE NAME: TURKEY
MAX RUN TIME: 20
DATA
Another program .called RSTORE is'similar, but. has
more extensive capabilities for storing information
about the sample, etc. and works with new and old data
files.
INTEGRATION TIME AS A FUNCTION
OF SIGNAL STRENGTH (IFSS)
The IFSS mode is a signal optimization mode which
is used when the operator wants the system to adjust
the Integration time as a Function of the Signal
Strength. The use of this option results in a nearly
constant signal-to-noise ratio and reduces the chances
of saturation of the detector. Figure 2.6 is a flow chart
of the IFSS algorithm. The dialogue begins when the
operator responds to the computer prompt SELECT.
MODE by entering IFSS. The other prompts have the
same significance as in the control mode except for the
following:
MAXIMUM REPEAT COUNT: This input (from 1
to 4096) specifies the maximum number of times to
repeat the specified base integration time if the signal
level does not reach the specified upper threshold. In
effect, this input coupled with the base integration time
allows the operator to specify a maximum integration
time (maximum repeat count x base integration
time = maximum integration time).
BASE INTEGRATION TIME: The operator
responds by entering a number from 1 to 4096, which is
the time in milliseconds desired for base integration
:ime. Generallv a low base integration-time (1-4) is
desirable in order to avoid saturation of the detector.
REPEAT COUNT BEFORE CHECKING LOWER
THRESHOLD: This input (from 1 to 8) specifies the
lumber of times to repeat the base integration time
aefore testing the lower threshold value.
[f the signal strength for a given ion has not reached the
lower threshold value, then the integration moves onto
the next higher mass ion. This, in effect determines the
minimum integration time (repeat count before check-
ing lower .threshold x base integration
time = minimum integration time).
LOWER THRESHOLD: This value determines the
point at which the program ceases the sampling of a
: given ion when a weak signal occurs. The program
collects the signal for the minimum integration time,
then if the lower threshold has not been attained,
integration continues at the next higher mass. A value
from 1 to 8 must be entered. These values correspond to
the strength of the signal required to continue
integration at a given mass (1 = 0% full scale,
2 = '0.025%,' 3 =0.05%, ' 4 = 0.10%,
5 = 0.20%, . 6 = 0.39%, 7 = 0.78%,
8 = 1.56%). An entry of 1 would mean that
integration would continue for the maximum
integration time or until the upper threshold is
attained.
UPPER THRESHOLD: This value determines the
point at which the sampling of a given ion ceases when
a strong signal occurs. The program collects the signal
until the upper threshold limit is attained or the
maximum integration time is reached (whichever
occurs first), then continues to the next higher mass.
The values (1 to 8) correspond to the signal strength
required for integration to stop (1 = 50% full scale,
2 = 25%, 3 = 12.5%, 4 = 6.25%,5 = 3.12%,
6 = 1.56%, 7 = 0.7%, 8 = 0.39%). An entry of 1
would mean that, for those signals where the lower
threshold has been attained, integration would
continue until the signal was 50% of full scale or until
maximum integration time is reached.
Numerous specific applications of these operating
parameters are contained in Chapter 3 with the
appropriate sample preparation methods. The
PERCAL program described above also applies to
IFSS parameters.
21
-------
4,193,280
SATURATION
SAVE ACTUAL REPEAT
COUNT FOR
NORMALIZATION OF MASS
SPECTRUM,CLEAR INTEGRATOR
! 6.25'% OF SATURATIONS)
INTEGRATE FOR A SHORT
-2 M SEC )
BASE INTEGRATION
TIME
HAS
SIGNAL REACHED
UPPER
THRESHOLD
UPPER
THRESHOLD
LOWER
THRESHOLD
UNT BEFORECHECKIN
HAS
MAXIMUM
COUNT BEEN
REACHED
(O.I % OF SATURATION-4
0.025% OF SATURATION
LOWER THRESHOLD
UPPER THRESHOLD
BASE INTEGRATION TIME
MAXIMUM REPEAT COUNT
REPEAT COUNT BEFORE
CHECKING LOWER THRESHOLD
. Figure 2.6 The IFSS algorithm flow chart
22
-------
2.8 MASS SPECTROMETER
SHUT-DOWN
SHORTTERM
When the system is to be shut down for short periods
of time (overnight, weekends, etc.) the following
procedure is recommended:
1. Turn ionizer off. Turn electron multiplier
voltage power supply to off or standby. Turn
RF/DC power supply to standby (1015).
2. Depress HALT switch on computer. Set the
LOAD-RUN switch to LOAD and wait for
the white LOAD light to signal that the disk
has stopped spinning. Shut down computer
terminal and other data output devices. Turn
computer power key to OFF.
3. Remove beam from oscilloscope with vertical
control or on/off switch.
4. If a diverter valve is present, direct the carrier
gas from the mass spectrometer. If no diverter
valve is present, one option is to disconnect the
column and cap the GC inlet. This allows the
spectrometer vacuum system to pump out
residual background under a high vacuum. A
fritted disk filter in the bulkhead union
provides adequate protection from separator
clogging during' column disconnect.,
Alternatively, one may reduce the flow
through the GC column to about
lOml/minute, but not disconnect it from the
separator. This provides some protection
against oil backstreaming into the analyzer in
the event of a power failure. Leave the column
oven temperature at least 50C below the
maximum operating temperature to minimize
column bleed.
LONGTERM
When the system is to be shut down for long periods
of time or for maintenance purposes (changing
separator, cleaning rods, etc.) the following procedure
is recommended:
1. Proceed as for short term shutdown.
2. Turn RF/DC line power switch to off (1015).
3. Remove GC column and cap the separator
port. Cool column and turn off helium flow
through the GC.
4. Turn power off/protect/protection override
switch on the vacuum controller to off. This
turns off the diffusion pumps, but the
mechanical pumps will remain on.
5. Wait at least 45 minutes for the diffusion
pumps to cool. Check to make sure that the
diffusion pump base is cool to the touch.
6. To vent the system when a solid inlet is
present, insert a hose from the regulator on a
cylinder of dry helium or nitrogen into the
solid inlet assembly. Set no more than 5 psi
pressure from the regulator. Tighten the
retaining knob on valve assembly. Open both
the ^ high vacuum and analyzer valves
simultaneously (slowly). When the valves are
partially open (you will be able to hear the
mechanical pumps pumping the venting gas),
throw the main circuit breaker on the vacuum
controller to shut off the mechanical pumps.
Open the valves 'all the way, allow the system
to fill with helium, and then remove the gas
line and close the solid inlet valve.
Exposure of the copper-beryllium electron multiplier
to air for extended periods of time (15 minutes or
longer) will result in rapid loss of multiplier gain. The
multiplier may be damaged permanently. Continuous
dynode electron multipliers are not affected by
exposure to air. It is recommended that Cu-Be electron
multipliers be stored in an inert gas atmosphere or a
vacuum desiccator.
-------
The sample preparation methods in this chapter
emphasize the broad spectrum approach explained in
chapter 1. There are no methods that are optimized for
a specific compound (parameter) or a closely related
group of compounds. Each method is a generalized
module with a scope and limitations. Several different
modules must be applied to cover the broad range of
several hundred thousand compounds that could
contribute to the pollutants in any specific sample. In
some cases there is significant overlap in the scope of
the modular methods. The appropriate choice of a
specific module will depend on the objectives of the
survey and the scope and limitations of the method.
Clearly there are deficiencies in some of the methods
and some environmentally significant compounds may
never be amenable to analysis by any method in this
chapter. For these classes of compounds, -major
innovations are required such as the development of
liquid chromatography methods. For the present these
problems are beyond the scope of this manual.
Many of the methods in this chapter are flexible in
that they can be combined or shortened, altered at
various stages to fit specific needs, or expanded to cover
unanticipated contingencies. Innovation in using these
procedures is encouraged insofar that it will improve or
otherwise make a particular analysis more efficient.
Hopefully, these procedures, in one form or another,
can be used for the majority of analyses that confront
the GC/MS laboratory.
All of the methods were designed for compatibility
with existing GC/MS systems. This is particularly
noticeable in the choice of solvents, since some solvents
cause excessive pressures in some mass spectrometers
and can cause an automatic shut down of the high
vacuum system. Generally all methods are designed to
be as simple as possible. The reliable qualitative
information inherent in the GC/MS method precludes
the need for a great deal of clean-up in most samples.
Simplicity in methods minimizes the chances of
contamination from reagents and glassware. However
where appropriate, as in fatty tissue and sediment
analyses, fractionation procedures are included in the
methods.
Recovery data on spiked samples is presemed with
many of the methods. It should be recognized that
these values reflect the best effort of a skilled and
experienced laboratory scientist in one or two
laboratories. These data do not guarantee that similar
values will be obtained in other laboratories.
Recoveries of spikes must be determined in each
laboratory as part of the quality assurance protocol of
the method if the data are used for concentration
measurements.
All of the methods in this chapter were contributed
by EPA laboratories. Many were developed or evolved
because of the need to have methods oriented to
GC/MS that can be used for a particular type of sample
or group of compounds.
The majority of the methods are for organics in
water, but that is not to imply that analyses of organics
in air, sediment, and fatty tissues are less important. In
reality, there are fundamentally, no differences in the
GC/MS aspects of the analyses of environmental
samples from different media. The principal differences
are in the sampling techniques and preliminary
separation procedures. Therefore much of the
information found in the section on water samples is
applicable to samples from other media. References to
these sections are included in the sections on air,
sediment, and fatty tissue samples.
In the interest of consistency, each ..method is
described in a similar format. The first part of the
method contains a brief definition of the method,
advantages and disadvantages, scope and limitations,
the rationale for the choices of materials and reagents,
detection limits, recovery efficiencies, and any special
problems with the method. All detection limits are
expressed in terms of a 33-450 amu mass spectrum with
average noise <1% of the base peak. A reagents
section is included if reagents are required with
emphasis on the purification of materials. An
equipment section lists and describes unusual or new
24
-------
equipment only. There is no listing of standard,
conventional glassware and other equipment that
should be found in any well equipped laboratory. The
procedure section is a step-by-step account of the
method itself including unusual sampling and storage
considerations, cleaning of glassware and sample
containers, requirements for blanks and spikes, GC
column selection, temperature programming and other
GC conditions, and sample computer dialogue for the
GC/MS data system.
3.1 WATER SAMPLES
Water samples encompass a wide variety of types
including processed water for human consumption,
lake water, river water, ground water, leachate,
municipal wastes, industrial wastes, and treated wastes.
Each of the sample preparation methods is applicable
to one or more of the water sample types and many
references to these applications appear in the following
sections.
DIRECT AQUEOUS
INJECTION INCLUDING
CONCENTRATION TECHNIQUES
Direct aqueous injection is the introduction of a few
microliters of water sample into the GC/MS system.
This procedure allows the identification of compounds
that are not amenable to other methods because they
are too water soluble.
The minimum detectable concentration using direct
aqueous injection is 1 to 5 mg/1 (ppm) depending on
the compound observed. The method is suitable for
analysis of many types of samples, expecially industrial
and municipal wastes.
The following types of compounds can be detected
by GC/MS using the direct aqueous injection
procedure: aliphatic hydrocarbons Cl - C7;
aromatic hydrocarbons-up to short chain alkylated
benzenes; the more volatile alcohols, glycols,
aldehydes, ketones, ethers, fatty acids, esters, amines,
amides, and halogenated compounds.
Simple distillation can be used to concentrate water
samples for direct aqueous injection. This technique
has been used to concentrate alcohols, ketones, amines,
nitiles, dioxolanes, and pyridines. Chlorinated solvents
such as methylene chloride and chloroform also have
been identified in distillates of industrial effluents.
Table 3.1 shows examples of recoveries of known
amounts of several compounds from a waste sample
after simple distillation. Approximately 10% of the
spiked solution was distilled.
The minimum detectable quantity is lowered by
distillation to about 1-10 ug/1 in the original sample. It
may be necessary to concentrate several liters of water
for situations such as the analysis of drinking water
where taste and odor problems have been observed.
.This can be done by using a large distillation flask or by
distilling several portions of the sample 'and
compositing the distillates for a final distillation in a
semi-micro apparatus. This allows a detection limit
lower than 1 ug/1 for some compounds.
Table 3.1. Recoveries of Spiked Organics from Water After a Simple Distillation.1
Compound Added
methanol
acetonitrile
propionaldehyde
methyl ethyl ketone
1,4-dioxane
n-butanol
aniline
isopropanol
nitrobenzene2
o-toluidinej
di-n-propylaminej
di-n-butylamine1
Number of
Replicates
4
4
4
4
4
6
5
4
1
1
1
1
Average
% Recovery
31
44
70
69
23
56
12
54
57
20
60
68
'Five hundred ml of boiled distilled waste was spiked at 0.2 mg/1 with the indicated organic chemicals. 'The spiked water was made
strongly basic.
25
-------
A simple evaporation technique is useful for
concentrating organic compounds whose boiling points
are too high for steam distillation. This has been
applied to the identification of ethylene glycol in water.
No special equipment is required for direct aqueous
injection. The distillation concentration technique
requires a conventional, all-glass laboratory still with a
1-3 liter capacity.
Install a conditioned column in the gas
chromatograph. Special care should be taken to flush
the column sufficiently with helium to remove any
residual air from the packing before heating. Be sure
the column was conditioned to minimize bleed during
the sample run. Columns which are applicable to direct
aqueous analysis are listed in Table 2.7. Temperature
programming from 70C to 220C at 8 degrees per
minute may be utilized. Inject 2-8 microliters of the
water sample with the ionizer off. With the pressure
about 10"5 torr, turn on the ionizer, start data
acquisition, and begin temperature programming. Halt
data acquisition after about 35 minutes.
Either the control mode or the IFSS mode may be
used for data acquisition. The sample dialogue below
contains some suggested parameters.
SELECT MODE: CONTROL
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME: CURRENT FILE
FILE NAME: UP TO SIX CHARACTERS
MASS RANGE: 20-260
INTEGRATION TIME: V7
SAMPLES/AMU: j_
THRESHOLD: press return
RT ON CRT?: N_
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
MASS RANGE: 20-260
SAMPLES/AMU: 1_
MAX RPT COUNT: 32
BASE INTEGRATION TIME: 1
RPT COUNT BEFORE CHECKING LOWER
THRESHOLD: 8
LOWER THRESHOLD: 4_
UPPER THRESHOLD: 4_
RT ON CRT?: N^
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
If no peaks are observed, a concentration procedure
may be applied. For distillation of industrial effluents.
transfer 500 ml of sample to a one liter distillation flask,
add boiling stones, and collect 25-30 ml of prime
distillate. This prime distillate may be redistilled in a
semi-micro distillation apparatus with the collection of
one ml of secondary distillate. The prime or secondary
distillate is analyzed by direct aqueous injection as
above.
For distillation of samples that are suspected to
contain less than one ug/1 of an organic compound,
collect only 10-15 ml during the first distillation.
Discard the pot residue and add an additional two liters
of sample. Distill as above and composite the prime
distillates .by collecting the second 10-15 ml in the same
collection flask.
A simple evaporation may be accomplished in a
beaker or evaporating dish on a hot plate. The residue
in this case is analyzed as above.
INERT GAS PURGING AND TRAPPING
Gas purging and trapping is a method for the
isolation, concentration, and determination of low
boiling organics in water. The method uses finely
divided gas bubbles passing through the water sample
to transfer organic compounds from the aqueous to the
gas phase. The compounds concentrate by adsorption
on a porous polymer trap at room temperature as the
purge gas is vented. The compounds are subsequently
desorbed at elevated temperature by backflushing with
a carrier gas into the gas chromatographic system. The
method may provide both qualitative and quantitative
information. Purging may be accomplished at ambient
or elevated temperatures with helium or another inert
gas.
Equipment. The equipment required for this method
consists of a purging device, a trap, and a trap heater or
desorber. Figure 3.1 shows construction details for an
all glass purging device with a 5 ml sample capacity.
26
-------
OPTIONAL
FOAM TRAP
EXIT 1/4
IN. O.O.
*- 14MM. O.D.
INLET 1/4
IN. O.D.
1 4 IN.
O.D. EXIT
10MM. GLASS FRIT
MEDIUM POROSITY
SAMPLE INLET
2-WAY SYRINGE VALVE
17CM. 20 GAUGE SYRINGE NEEDLE
6MM.O.D. RUBBER SEPTUM
10MM. O.D.
INLET
1/4 IN. O.D.
1/16 IN. O.D.
STAINLESS STEEL
13X MOLECULAR
SIEVE PURGE
GAS FILTER
PURGE GAS
FLOW CONTROL
Figure 3.1 A Purging Device with a 5 ml Sample Capacity.
27
-------
The glass frit at the base of the sample volume allows
the finely divided gas bubbles to pass through the
sample while the sample is restrained above the frit.
Gaseous volumes above the sample are kept to a
minimum to eliminate dead volume effects, yet
sufficient space is allowed to permit most foams to
disperse. The inlet and exit ports are constructed of
heavy walled quarter inch glass tubing to permit leak
free removable connections with finger tight
compression fittings containing Teflon ferrules. The
removeable foam trap is optional and recommended for
samples that foam. A 25 ml capacity purging device is
recommended for use with a mass spectrometer GC
detector.
Figure 3.2 shows a trap which is a short gas
chromatographic column that retards the flow of the
compounds of interest at ambient temperature while
venting the purge gas and, depending on the adsorbent
used, much of the water vapor. The trap is constructed
with a low thermal mass to allow rapid heating for
efficient desorption, and rapid cooling to ambient
temperature for recycling. The trap length, diameter,
and wall thickness indicated in Figure 3.2 are critical
and variations in these will affect the trapping and
desorption efficiencies of the compounds discussed in
this section.
The trapping and desorption efficiencies are also a
function of the adsorbents, adsorbent mass, and the
adsorbent packing order shown in Figure 3.2. The
single adsorbent Tenax GC (60/80 mesh) is effective
for compounds that boil above approximately 30C.
However compounds that boil below approximately
30C are not strongly adsorbed by Tenax and may be
vented under the purging conditions. If compounds
that boil below about 30C are to be measured, a dual
adsorbent trap should be used. Grade-15 silica gel
effectively retards the flow of most organics at ambient
temperature and should be packed behind the Tenax to
trap the lower boiling components. Silica gel is not a
useful single adsorbent because higher boiling
compounds do not efficiently desorb from it at 180C.
The Tenax-silica gel combination trap utilizes the
adsorptive properties of two materials to provide a trap
that effectively adsorbs and desorbs a wide variety of
organic compounds. The small amount of OV-1 on
glass wool at the trap inlet (Figure 3.2) is to insure that
all the Tenax adsorbent is within the heated zone and is
efficiently heated to the desorption temperature. A
metal fitting at the trap inlet could act as a heat sink
and create a cool spot on the Tenax if this spacer is not
used.
Details of the trap heater are also shown in Figure
3.2. The adsorption-desorption cycle may be
accomplished conveniently with the use of a six port
valve and plumbing system constructed of materials
that neither adsorb volatile organics nor outgas them.
Several commercially available purge and trap systems
use this approach. With the six port vaJ,ve in the adsorb
position, the effluent from the purging device passes
through the trap where the flow of the organics is
retarded and the purge gas is vented. During this
period the gas chromatograph is supplied with carrier
gas and may be used for other analyses. With the valve
in the desorb position, the trap is placed in series with
the gas chromatographic column which allows the
carrier gas to back flush the trapped materials onto the
chromatographic column.
It is strongly recommended that the power for the
desorber heater be supplied by an electronic
temperature controller that is set to begin supplying
power as the valve is placed in the desorb position. This
allows rapid heating of the trap to 180C with minimal
overshoot and maintenance of the desorb temperature
until desorption is complete (a four minute backflush at
20-60 ml/min is recommended). Using this procedure,
the trapped compounds are released as a narrow plug
into the gas chromatograph, which should be at the
initial operating temperature. Packed columns with
theoretical efficiencies near 500 plates/foot under
programmed' temperature conditions can usually
accept such desorb injections without altering peak
geometry.
Substitution of a non-controlled power supply, such
as a manually operated variable transformer, will cause
non-reproducible retention times and may lead to
unreliable concentration measurements. If it is not
possible to heat the trap in a rapid and controlled
manner to the desorption temperature, the contents of
the trap may be transferred onto the analytical column
at 30C or lower and once again trapped. The analytical
column is then rapidly heated to the initial operating
temperature for the analysis.
Several gas chromatographic columns have been
employed for the separation of the volatile components
prior to measurement. A recommended column for
general purpose work is a 8-ft x 0.1-in. id stainless steel
or glass tube packed with 0.2% Carbowax 1500 on
Carbopack-C (80/100 mesh). With a helium flow of 40
ml/min., the initial temperature of 60C is held for three
min., then programmed at 8C/min. to 160C.
Newly packed traps should be conditioned overnight at
230C with an inert gas flow of at least 20 ml/min. The
trap is also conditioned prior to daily use by
backflushing at 180C for 10 min.
28
-------
PACKING PROCEDURE
CONSTRUCTION
DUAL A
GLASS WOOL 5MM
OSAOE IS
SIUCA GEL
8CM
TENAX ISCM
17. OV-I ICM
GLASS WOOL
SMM
ia;
oso
//
k
M
1
1
>$
If
^
1
-: -T.
1
if ir
»iNT SINGLE
GLASS WOOL SMM
TENAX J3CM
37. OV-I ICM
GLASS WOOL
SMM
(LET
A
TIJ
9SO
%
\
1
|
1
1
1
^
;'«
1
\
kf i
HUNT
411
COMPIISSION nnrno NUT
AND FEMUIEI
MFT. PVFOOT BISISTANCE
WIKf WIAPKO SOUO
TNIIMOCOUKE/CONTIOILIR
SINSOI
TUMNO 3SCM 0.10) IN. 1.0.
0.1JJ IN. O.D. STAINLESS STia
Figure 3.2 The Trap Assembly for a Purging Device
29 '
-------
Discussion. Table 3.2 contains a list of some of the
compounds that have been submitted to this type of
analysis. The recovery data is intended to be illustrative
only since recoveries depend strongly on several
important method variables. Recoveries are expressed
as a percentage of the'amount added to organic free
water. The purge time was 11-15 minutes with helium
or nitrogen, the purge rate was 20 ml/minute at
ambient temperature, and the trap was Tenax followed
by Silica Gel. Data from the 5 ml sample was obtained
with a custom made purging device and either flame
ionization, microcoulometric, or electrolytic
conductivity GC detectors. Data from the 25 ml
sample was obtained with a Tekmar commercial liquid
sample concentrator and a mass spectrometer GC
detector using continuous repetitive measurement of
spectra.
A number of other compounds have been
concentrated and measured using the purge and trap
method, but no recovery data for these is available.
These compounds include chloromethane,
bromomethane, chloroethane, 1,2-dichloropropane,
trans-1,3-dichloropropene-1, cis-1,3-dichloropropene-
1, 1,1,2-trichloroethane, 2-chloroethylvinylether,
1,1,2,2-tetrachloroethane, and ethylbenzene. In general
the method is applicable to compounds that have a low
solubility in water and a vapor pressure greater than
water at ambient temperature.
All of the experiments summarized in Table 3.2 were
conducted with the water sample at ambient
temperature, about 22C. Purging at elevated
temperatures has been investigated and clearly affects
recoveries of some compounds. However, this is not
recommended as a general procedure because the
elevated temperature may promote chemical reactions
that could significantly alter the composition of the
trace organics. This is especially important with
chlorinated drinking water or waste effluents.
A significant method variable is the purge gas flow
rate. The total purge time is not very flexible since it
will usually be desirable to keep this as short as possible
to minimize the analysis time. In all of the experiments
summarized in Table 3.2, a flow rate of 20 ml/min.. was
employed for 11-15 minutes, and for many compounds
an acceptable recovery was obtained. Figure 3.3 shows
the percentage recovery of several representative
compounds as a function of purge gas flow rate. The
general curve shape displayed for 1,2-dichloroethane
and bromoform is typical of most of the compounds in
Table 3.2. The low boiling compound vinyl chloride
was trapped on Tenax only and its flow rate curve
illustrates the sharp reduction in trapping efficiency
observed with this type of compound and trap at
elevated flow rates. . The compound
dichlorodifluoromethane displays a similar flow rate
curve even with the combination Tenax-silica gel trap.
Because of the differences in the construction of
various purge and trap devices, actual recoveries may-
vary significantly from those shown in Figure 3.3 and
Table 3.2. Therefore, it is required that individual
investigators determine recoveries of compounds to be
measured as a function of flow rate with their
apparatus. Operation in the optimum flow rate range
will assure maximum sensitivity and precision for the
compounds measured.
The recoveries of aliphatic hydrocarbons were found
somewhat more variable than the recoveries of the
other compounds investigated with this method. In all
of these experiments, known quantities were added to
organic free water, and the slightly soluble aliphatic
hydrocarbons probably formed a thin surface layer on
the water. Under these inhomogeneous conditions,
special care is needed to achieve consistent results.
In order to generate quantitative measurements
within a reasonable purge time, e.g. 10-15 min.,
calibration of the method with known standards is
required. The recommended approach is to estimate
the concentration of the unknown by a comparison of
its peak size with the size of the corresponding peak in a
quality control check standard made at some
appropriate concentration level and measured at
regular intervals during the work day. From this
estimate a concentration calibration standard is
prepared with the concentrations of the compounds to
be measured within a factor of two or less of the
probable concentration in the unknown. Standards are
prepared by taking aliquots of solutions in methanol
and injecting them into organic free water. This insures
maximum dispersal of the organic compound in the
aqueous system. Organic free water is prepared by
passing distilled water through an activated carbon
column.
The standard is purged and measured immediately
after the unknown and under the identical conditions
used with the unknown. A sample of organic free water
should be purged between each set of samples and
especially after all high level standards or samples. This
will insure that the apparatus is purged of contaminats
and prevent cross contamination.
Sample matrices significantly different than surface
water have not been investigated extensively. Extremes
of pH, high ionic strength, or the presence of miscible
organic solvents will likely affect recoveries of some
compounds. Therefore measurements of compounds in
30
-------
Table 3.2. Recoveries of Organics by Gas Purging and Trapping.
Amount
Added
ug/1
% Re-
covery
5ml
Sample
Amount
Added
ug/1
% Re-
covery
25 ml
Sample
Chlorinated Hydrocarbons
methylene chloride 12 97
chloroform 160 101 12 95
chlorodibromomethane 8,2 86,69 12 72
bromodichloromethane 40,2 94,82 12 72
carbontetrachloride 4,2 108,82
1,2-dichloroethane 2 70 12 95
1,1,2-trichloroethylene 2,2 118,89
tetrachloroethylene 2,2 81,80
chlorobenzene 4 80
p_-dichlorobenzene 4 71 12 58
dichlorofluoromethane 2 7
trichlorofluoromethane 2 99
vinyl chloride 2 95
1,1-dichlofoethylene 2 114
1,1-dichloroethane 2 90
trans- 1,2-dichloroethylene 2 100
1,1,1-trichloroethane 2 88
dichloroiodomethane 2 72
2,3-dichloropropene-l 2 85-
Hydrocarbons
n-pentane 81 100
n^nonane 93 99
n-pentadecane 100 56
benzene 12 105
toluene 12 91
Brominated Hydrocarbons
bromoform 4,2 67,48 12 73
1,2-dibromoethane 4,2 80,47
Nitrogen Compounds
nitromethane 24 2
nitrotrichloromethane 24 22
N-nitrosodimethylamine 24 0
N-nitrosodiethylamine 12 0
N-nitrosodi-n-butylamine 12 0
31
-------
BROMOFORA
1,2-DJCHLOROETHANE
DieHLORODiFLUOROMETHANE
VINYL CHLORIDE o
FLOW RATE ml/min.
Figure 3.3 Recoveries of Selected Compounds as a Function of Purge Gas Flow Rate.
32
-------
these matrices must include determinations of
recoveries of spikes in the sample matrix and perhaps
use of a calibration based on the method of standard
additions.
The detection limit of the method is also dependent
on a number of operational variables. For a sample
volume of 5 ml a concentration factor of about 1000
over a direct aqueous injection is usually possible. This
places the limit of detection in the 0.1 to 1 microgram
per liter range for a GC/MS system operating in the
selected ion monitoring mode. With a GC/MS system
operating in the continuous repetitive measurement of
spectra mode, a sample volume of 25 ml is
recommended to achieve this detection limit. The
method can be applied over a concentration range of
approximately 0.1 to 1500 micrograms per liter. Figure
3.4 shows a chromatogram of a mixture of 29
compounds from a purge and trap analysis.
Sample Collection and Preservation. Previous
reports emphasized the importance of sample handling,
and indeed because of the very volatile nature of the
compounds measured in this type of analysis, sample
collection deserves special consideration. In general,
narrow mouth glass vials with a total volume in excess
of 50 ml are acceptable. The bottles need not be rinsed
or cleaned with organic solvents, but simply cleaned
with detergent and water, rinsed with distilled water,
air dried, and dried in a 105C oven for one hour. The
vials are carefully filled with sample to overflowing
(zero head space) and a Teflon faced silicone rubber
septum is placed Teflon face down on the water sample
surface. The septa may be cleaned in the'same manner
as the vials, but should not be heated more than one
hour because the silicone layer slowly degrades at
105C.
faced septa are acceptable if the seal is properly made
and maintained during shipment. However, several
years of experience indicates a success rate significantly
less'thant 100% in making proper seals of this type in
the field. Therefore simple screw cap vials used with the
Teflon faced septa were evaluated and found to give
equivalent results and a very high rate of acceptable
samples. Narrow mouth screw cap bottles with Teflon-
faced silicone rubber septa cap liners are strongly
recommended for sample collection.
One special problem in sample preservation has been
recognized as a result of the widespread application of
this method to drinking waters which contain residual
quantities of disinfectants, e.g., chlorine. The levels of
certain chlorinated compounds, e.g., chloroform,
found in such waters will vary depending on the time of
analysis unless the residual chlorine is consumed by a
reducing agent such as sodium thiosulfate. Table 3.3
shows the concentrations of four compounds in
Cincinnati tap water as a function of the sample age in
days. The samples were taken from the distribution
system at the EPA Environmental Research Center
and maintained at 4C until analyzed. No reducing
agent was added to the samples.
The data in Table 3.3 shows that under the
experimental conditions used the chloroform
concentration increased by 114% during the eight day
,. -storage period. Smaller increases in the concentrations
' of the brominated compounds were observed, but the
carbontetrachloride concentration did not change
within the precision' of the method which averages
approximately 6% in the 1-1000 ug/1 range. A similar
set of samples was stored at 22C, and the same trends
were observed except the concentrations of each of the
halomethanes after seven and eight days were the same
within the precision of the method. This indicates that
Table 3.3 Effect of Residual Chlorine on Concentrations of Chlorinated Methanes in
Drinking Water at 4C
Time,
days
0
1
2
7
CHC1,
ug/1
. 17.0
17.9
23.7
32.6 .
36.3
CHBrCU
ug/1
12.4
12.9
16.1
19.9
21.6
Two types of seals for the vials have been employed
and both give satisfactory results. Aluminum, one-
piece, crimp-on seals used with serum vials and Teflon
CHBr;Cl
ug/1
11.9
11.7
14.4
17.2
18.7
ecu
ug/1
3.1
3.1
3.4
3.4
3.5
the rate of hafogenation was reduced substantially after
one week of storage at 22C. The reduced rate of
reaction was presumed due to a greatly diminished
33
-------
COLUMN: 0.27. CABBOWAX 1500 ON CARBOPACK-C
PROGRAM: 60°C-3 MINUTES e'/MINUT! TO 160'C
S
at
O
Lk
O
O
RETENTION TIME MINUTES
Figure 3.4 Chromatogram of Organohaiides.
34
-------
concentration of active halogenating agents, or the
organic substrates, or both, but the details were not
investigated further. In a third set of samples the
reducing agent sodium thiosulfate was added at the
time of sampling to quench the halogenation reaction.
The concentration of the halomethanes in these
remained constant within the precision of the. method
over the eight day period. In these samples no
significant losses were observed indicating the
effectiveness of the sample sealing procedures
described in this paper.
The designer of an analytical survey that will include
samples containing residual 'chlorine or other similar
agents must be aware of these effects. The addition of a
reducing agent at the time and place of sampling will
give a measure of the instantaneous concentration of
halogenated compounds, and this may or may not be
the desired value. A measure of the maximum possible
concentration of halogenated species in the particular
sample may be obtained by storing the sample at 22C or
higher until the concentration of halogenated
compounds is constant.
Procedure. The following procedure will apply to
both commercially available purging instruments and
home-made units. However, home-made units usually
demand trap manipulation which will not be discussed.
1.
i
Adjust the helium flow through the purging
vessel to 40 ml/min.
Newly packed traps must be conditioned at
approximately 230C with a helium flow of 40
ml/min for 16 to 24 hours. Each day before
use, the trap should be conditioned at 180C for
10 minutes during a backflush with helium at
30 ml/min.
Inject 25 ml of sample into a 25 ml purging
device with a syringe. A sample volume of 25
ml is recommended when GC/MS is used for
identification and measurement of the
purgeable compounds. For more concentrated
samples, a 5 ml volume can be used.
Purge the sample for 12 minutes at 40 ml per
minute at room temperature.
After the 12 minute purge time, desorb the
trapped compounds onto the GC column
which has been cooled to room temperature
for 10 minutes. Desorption is accomplished by
rapidly heating the trap to 180C while
backflushing with helium at 30 ml per minute
for 4 minutes.
6. When the transfer is complete, heat the GC
column rapidly to the initial operating
temperature for analysis. Temperature
programming at a suitable rate (4-8 degrees
per minute) should be used to obtain sufficient
resolution between GC peaks and accurate
mass spectra.
7. Either the control mode or the IFSS mode may
be used for data acquisition.
The sample dialogue below contains some suggested
operating parameters.
SELECT MODE: CONTROL
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME: CURRENT
FILE
FILE NAME: UP TO SIX CHARACTERS
MASS RANGE: 20-260
INTEGRATION TIME: \1_
SAMPLES/AMU: J_
THRESHOLD: press return
RT ON CRT?: N_
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
. DELAY BETWEEN SCANS (SECS.)?:
press return .
SELECT MODE:,, IFSS
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME:
CURRENT FILE
FILE NAME: UP TO SIX CHARACTERS
MASS RANGE: 20-260
SAMPLES/AMU: J_
MAX RPT COUNT: 32
BASE INTEGRATION TIME: j_
RPT COUNT BEFORE CHECKING
LOWER THRESHOLD: 8_
LOWER THRESHOLD: 4_
UPPER THRESHOLD: 4_
RT ON CRT?: N_
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS-'(SECS.)?:
press return
35
-------
QUALITATIVE HEADSPACE ANALYSIS
Headspace analysis is a method of measurement for
compounds that have a relatively high vapor pressure
over a water sample. The primary purpose of the
method is qualitative, analysis because accurate
concentration measurements require extensive
information about the equilibria of many compounds
between the vapor and dissolved phases. The principal
advantage of the method is that it permits the rapid
identification of very volatile compounds, e.g., vinyl
chloride, fiuorocarbons, etc., that may be missed with
some other methods.
Samples should be collected in bottles as described in
the inert gas purge and. trap procedure. However, in
place of the standard screw-on caps, the open top caps
should be used. This permits sampling of the headspace
without removing the screw-on cap. Glassware for
blanks and samples should be prepared as described in
the purge and trap procedure. In the laboratory, prior
to sample collection, prepare a blank by completely
filling a sample bottle with low-organic water. Low-
organic water is prepared by passing distilled water
through an activated carbon column and" purging the
carbon-treated water with an inert gas. The filled
bottles are sealed and shipped to the sampling site along
with the empty sample bottles. While samples are being
taken, the blank bottles are opened and about 2 ml of
water is decanted. The blank bottles are resealed and
returned to the laboratory. These blanks will
compensate for residual organics in the atmosphere at
the sampling site as well as contamination during
shipment and storage. Samples are taken by completely
filling the bottles, then decanting about 2 ml. The
bottles are capped, shipped at 0-5C, and the samples
analyzed within 48 hours.
For the analysis, place the sample bottles in a water
bath at 25C and allow temperature equilibration to
standardize the headspace measurement. During this
thermal equilibration, occasionally agitate the contents
of the bottle to promote equilibrium between the gas
and liquid phases. The GC columns suggested for
direct aqueous injection in Table 2.7 are also
recommended for the qualitative headspace analysis.
Flush a valve-controlled gas tight syringe twice with
helium. To sample the headspace, pull 2 ml of helium
into the syringe, close the valve, pierce the sample
bottle septum, and inject the helium into the headspace,
of the sample bottle. Without removing the needle from
the septum, pull the syringe barrel out to the 5 ml
mark, close the valve, and withdraw the syringe from
the septum. To inject into the chromatograph,
compress the gases in the syringe against the closed
valve to about 2 ml, insert the'needle into the injection
block, and open the syringe valve. After completing the
injection of a compressed plug of gas, close the valve
and withdraw the syringe. Initial column temperature
should be as near ambient as possible. A holding time
of several minutes is suggested followed by temperature
programming at 4-8 C/min. A sample run time of
about 30 min is usually 'sufficient. Suggested sample
data acquisition parameters are as follows:
SELECT MODE: .CONT
CALIBRATE?: N_
TITLE: UP TO 64 .CHARACTERS
CALIBRATION FILE NAME:
CURRENT FILE
FILE NAME: .UP TO 6 CHARACTERS
MASS RAN.GE: 14-16; 19-27:29-31;
33-260
INTEGRATION TIME T7;17;17;17
SAMPLES/AMU: 1;'1;1;1
THRESHOLD: press return
RT ON CRT?: N^
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: UP TO 64 -CHARACTERS
CALIBRATION FILE NAME:
CURRENT FILE
FILE NAME: UP TO 6 CHARACTERS
MASS RANGE: 14-16;19-27;29-31;
33-260
SAMPLES/AMU: 1;1;1;1
MAX RPT COUNT: 32
BASE INTEGRATION TIME: J_
RPT BEFORE CHECKING LOWER
THRESHOLD: 8_
LOWER THRESHOLD: 4_
UPPER THRESHOLD: J_
RT ON CRT?: N_
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
36
-------
EXTRACTION WITH A LOW BOILING
SOLVENT '
Liquid-liquid extraction with a low boiling solvent is
a time honored technique in organic analysis. The
principal advantages of this method are its applicability
to a broad variety of compounds and the large
concentration factors that may be realized. A
disadvantage is that very volatile compounds, e.g.,
chloroform, vinyl chloride, etc., will not be observed as
they are either lost during extract concentration or
masked during solvent elution from the GC.
The scope, limitations, and detection limits of the
method are a function of the solvent selected. Over the
years a great variety of solvents have been used. The
most popular low boiling solvents for liquid-liquid
extraction are diethyl ether, hexane, benzene, ethyl
acetate, carbon tetrachloride, chloroform, and
methylene chloride. Each of these solvents may be the
optimum for a given situation, but methylene chloride
is the only solvent recommended for general purpose,
broad spectrum extractions in this section. Among all
the solvents available it has the maximum number of
favorable properties.
Diethyl ether is a poor choice because it invariably
contains peroxides and these must be removed before
its' use. However, air oxidation of diethyl ether
produces more peroxides and, even immediately after
purification, sufficient concentrations are present-.to,
react with trace organics and solvent molecules to,
create an unacceptable reagent blank. On balance
diethyl ether, a hazardous flammable substance, is
simply not of sufficient value to justify its continued
use.
Hexane, benzene, and analogous hydrocarbon
solvents are insufficiently polar to extract efficiently a
wide variety of polar organics that are amenable to gas
chromatography. This makes them unsuitable for the
broad spectrum approach. Ethyl acetate is used in the
biomedical field for extractions of drugs from body
fluids, but it has not been evaluated sufficiently for
broad spectrum applications in water analysis. All of
the above solvents have the additional minor
disadvantage of being lighter than water which is an
inconvenience during separation of immiscible phases.
Carbontetrachloride is a carcinogenic material and
its human inhalation toxic dose is 20 ppm (central
nervous sytem effects). In addition its relatively low
polarity, relatively high boiling point, and relatively
high molecular weight make it clearly unsuitable for
GC/MS work.
Chloroform is reported to be carcinogenic and its
human inhalation toxic dose (systemic effects) is
10 ppm. By contrast, methylene chloride is not
carcinogenic and the corresponding toxic dose. for
methylene chloride is 500 ppm (central nervous system
effects). Of particular concern to GC/MS users is the
tendency of both of these chlorinated solvents to pass
through the sample/carrier gas enrichment device.
This causes the development of excessive pressures in
the mass spectrometer which may bring about an
automatic shut-down. One solution is the use of a
solvent venting valve. However if this is not available,
the replacement of the chlorinated solvent during the
concentration of the solvent extract is recommended.
Methylene chloride (bp 41C) is readily replaced by
acetone (bp 56C) but chloroform (bp 62C) is not. Up
to 8 ul of acetone may be injected into the GC/MS
without recourse to a venting valve. The lower boiling
point of methylene chloride gives it a major advantage
over chloroform in reducing losses of volatile organics
during extract concentration. Finally chloroform is not
suitable for methylations with diazomethane whereas
methylene chloride is a preferred solvent (see
section 3.5).
On balance, methylene chloride is the solvent of
choice for low boiling solvent extractions. It is
commercially available in very pure form, contains no
peroxides, has a very low boiling point, a low toxicity,
and a polarity sufficient to extract a wide variety of
polar organics! It is very insoluble in water, easily
replaced by acetone, and is generally recognized by
practicing chemists as the equivalent of chloroform for
solvent extractions. Some representative single
laboratory recovery data of spiked organics in distilled
water by solvent extraction with methylene chloride
are shown in Table 3.4. Additional classes of
compounds not included in Table 3.4 have been
observed by liquid-liquid extraction with methylene
chloride. These include aliphatic hydrocarbons,
benzene derivatives, organic phosphorous pesticides,
some carbamates, alcohols, aldehydes, ketones, some
carboxylic acids, esters, nitriles, sulfur compounds, and
many others.
The detection limits for .methylene chloride
extractions depend on the size of the water sample, the
extent of concentration of the extract, the extraction
efficiency of specific substances, and the GC/MS
behavior of the specific substances. With a three liter
water sample and concentration of the extract to
100 ul, the usual detection limit is in the range of
10-50 ng/1 (10-50 ppt) for compounds with a
favorable extraction efficiency (> 80%) and favorable
GC/MS behavior.
37
-------
Table 3.4. Recoveries of Organics by Solvent Extraction with Methylene Chloride
Compound Added., Spike Con., ug/1 pH' % Recovery
Chlorinated Hydrocarbons
Lindane
Heptachlor
DDD-p,p'
DDT-p,p'
Endrin
Toxaphene
Aroclor 1016
Aroclor 1254
hexachloroethane
p_-dichlorobenzene
bis(2-chloroisopropyl)ether
bis(2-chloroethyl)ether
Chlordane (technical)
Aldrin
Heptachlor epoxide
DDE-p.p'
Dieldrin
Aroclor 1242
hexachlorobenzene
m-dichlorobenzene
hexachlorocyclopentadiene
hexachloro- 1 , 3-butadiene
1 -chloro 4 nitrobenzene
Phenols
phenol
dimethylphenol
2,4,6,-trichlorophenol
pentachlorophenol
2-nitrophenol
o-chlorophenol
2
2
2
2
2
2
2
2
50
2
25
25
2
2
2
2
2
2
<^
z
2
2
25
2
5,25
2
2
.5
25
25
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
. N
N
N
N
N
A.A + N
N
N
A
N
N
100
90
97
98
105
106
75
80
45
103
84
88
88
94
95
104
84
84
84
70
55
69
80
52,59
75
53
65
52
30
Polycyclic Aromatic Hydrocarbons
naphthalene
acenaphthylene
acenaphthene
pyrene
fluoranthene
chrysene
benzofa]pyrehe
0.5
25
0.5,25
0.5
2
2
2
N
N
N,N
N
N
N
N
86
92
101,92
104
60
73
76
38
-------
Table 3.4. Recoveries of Organics by Solvent Extraction with Methylene Chloride (continued).
Compound Added Spike Con., ug/1 pH' % Recovery
Polycyclic Aromatic Hydrocarbons (continued)
indeno[l,2,3-cd]pyrene 25 N 59
phenanthrene 2 N 72
anthracene 2 N 88
dibenzo[a,h]anthracene 25 N 104
benzo[g,h,i]perylene 25 N 100
benzo[a]anthracene .25 N 100
fluorene 2 N 87
Nitrogen Compounds
pyridine 100 B 92
nitrobenzene 100 B 98
o-nitrotoluene 25 N 88
aniline 100 B 81
o^methylaniline 100 B 97
di-n-butylamine 100 B 20
benzidine 20 N 57
N-nitrosodimethylamine 20 A,B,N 0,0,0
N-nitrosodiethylamine 20 N 49
N-nitrosodibutylamine '20 N 73
2-benzothiazole 25 N 95
hydrazobenzene 25 N 84
Oxygen Compounds
n-hexanol 25 N 64
camphor 25 N 89
alpha terpineol 25 ' N 82
isobutyric acid 25 A 5
isovaleric acid .25 A 17
n-octanoic acid 30 N,A 86,15
methyl palmitate 25 N,A 72,31
n-tributyl phosphate 25 N 105
di(2-ethylhexyl)phthalate 2 N 95
dimethyl phthalate . 2 N 75
diethyl phthalate 2 N 87
di-n-butyl phthalate 2 N 92
isophorone 2 N 100
'N = pH 6-8; A = pH 2^t; B=pH 10-12.
39
-------
For accurate quantitative analysis as well as to
obtain additional qualitative information, known
quantities of compounds should be dissolved in acetone
and aliquots mixed with sample water. This spiked
sample is extracted according to the procedure to
determine the amount recovered and to verify that the
compound was extracted in the correct pH fraction.
For each, set of samples a reagent blank is required. A
reagent blank is defined as an experiment that uses all
procedures, quantities of materials, and glassware used
in sample preparation except that no water or aqueous
solution is used. It is required even when
contamination from glassware and reagents is well
controlled. The reagent blank result is the
documentation that proves that good control was
exercised, and it defines precisely the level of
background that was beyond control.
Reagents and Equipment. Redistill the methylene
chloride and acetone in an all-glass laboratory still
before use. Mesityl oxide (bp 129C) and diacetone
alcohol (bp 168C) are common contaminants in
acetone. The entire volume of the still pot should not be
distilled to prevent contamination of the distillate with
these higher boiling impurities. Also the pot residue
should be discarded frequently.
Distillation of solvents is particularly important for
analyses of relatively clean water, for example,
drinking water or water from a clean lake. Distillation
of methylene chloride and acetone (if used) should be
carried out immediately before use since these
compounds begin to develop low level impurities
within hours even when stored in the dark under
nitrogen. For waste effluents, the best available
commercial solvents may be adequate for use without
redistillation. This should be verified by GC/MS
analysis of a reagent blank prior to the extraction of the
samples.
Purify the sodium sulfate by extraction with 50
volume percent methylene chloride - acetone in a
soxhlet extractor for 8 hours. Air dry the sodium
sulfate and heat in a 120C oven for 4 hours.
Standard laboratory glassware is required for this
procedure. Extractions of 3 liter samples require a
6 liter separatory funnel with a Teflon stopcock.
Kuderna-Danish (KD) glassware is used for the
concentration of extracts. A standard set of KD
glassware consists of a 3 ball Snyder column, a 500 ml
evaporating flask, and a 10 ml receiver ampul
graduated in 0.1 ml increments. An all glass
laboratory still and a Soxhlet extractor are required for
purification of reagents.
Procedure. The following procedure is scaled to a
3 liter sample. This is most appropriate for relatively
clean water, for example drinking or clean lake water.
For effluents and similar water containing higher
concentrations, the quantities of sample and reagents
should be pealed accordingly. This procedure was
designed to isolate the neutral, acidic, and basic
compounds in three separate extracts, and the data in
Table 3.4 was obtained in this way. An alternative used
in the EPA sampling and analysis procedure for
screening of industrial effluents for priority pollutants
is to combine the basic and neutral compounds in a
single fraction by initial adjustment of the pH to 11 or
greater. This reduces the workload by one-third in that
two rather than three extracts must be processed, but
other complications that may result from this short-cut
are not well established.
Glassware for blanks, spikes, and samples should be
washed with detergent, rinsed with tap water, rinsed
with distilled water, air dried and heated in a muffle
furnace at a minimum temperature of 300C for one
hour. One gallon jugs for samples should be cleaned
using the same procedure. However, these jugs are
usually made of a soft glass and should not be heated as
rigorously as Pyrex glassware. Heating to 300C for
fifteen minutes is recommended. The sample jugs must
be supplied with Teflon cap liners.
1. Measure the pH of the gallon sample and
transfer 3 liters to a 6 liter separatory funnel. If
the pH is less than 6 or greater than 8, adjust
the pH to 6-8 with concentrated HC1 or
NaOH. Extract the sample with 125 ml of
methylene chloride with vigorous shaking for
3 minutes. Allow the layers to separate, then
drain the methylene chloride layer into a
suitable collection flask. Repeat twice with
75 ml portions of methylene chloride and
combine the three extracts.
If an emulsion develops, a number of
techniques may be applied to resolve the phase
boundary. Additions of reagents or heating the
mixture is not recommended as these actions
may cause more problems than they solve. One
effective emulsion breaking technique is to
drain off the emulsion, swirl several times in
the drain flask, and pour the mixture gently
through the water in the separatory funnel. If
this produces a partial methylene chloride
layer, separate the clear methylene chloride,
and pour the remaining emulsion through the
water until a satisfactory separation of layers is
accomplished.
40
-------
Pour the combined extracts through two
inches of anhydrous sodium sulfate in a
19 mm I.D. glass column. Collect the dried
extract in a 500-ml Kuderna Danish (KD)
flask fitted with a 10-ml ampul. A reagent
blank, treated exactly like the sample extracts,
should be run along with a sample or set of
samples.
After the combined extract has filtered
through the sodium sulfate, rinse the sodium
sulfate with 50 ml of acetone. This is done to
rinse any residual sample from the sodium
sulfate, and to introduce a nonchlorinated
solvent into the sample for GC/MS injection.
If the GC/MS system is equipped with a
solvent venting valve and it is known that
methylene chloride injections are well
tolerated, the acetone addition may not be
necessary.
Adjust the pH of. the water sample to 2 using
concentrated HC1 and repeat steps 1, 2, and 3
this time using 75 ml of methylene chloride
for each extraction. However, if a
derivatization procedure is to be employed, for
example the methylation of the acid fraction to
convert carboxylic acids to methyl esters, see
section 3.5 first.
Adjust the pH of the water sample to 12 using
saturated NaOH solution and repeat steps 1,2,
and 3 as in step 4. Three sample extracts are
now contained in three KD flasks: the
neutral compounds extracted from a solution
of pH 6-8, the acid compounds extracted from
a solution of pH = 2, and the basic compounds
extracted from a solution of pH=12. The
reagent blank is in a fourth KD flask.
Fit a 3 ball Snyder column to each Kuderna-
Danish (KD) flask and concentrate the
extracts on a steam bath to approximately
5 ml. After concentration the methylene
chloride (bp=41) will be completely removed
and the sample will be contained in acetone
(bp=56). The extract can be further
concentrated in the graduated ampul in a
warm water bath under a stream of clean, dry
air or nitrogen. Concentration of the extract to
100 ul or less is entirely possible with very low
losses. However, successful completion of this
final concentration requires tender loving care!
The temperature of the water bath must be no
higher than 50C, the stream of gas must be
truly gentle, and the inside walls of the ampuls
must be repeatedly rinsed with small quantities
of pure solvent.
7. Install a conditioned column in the gas
chromatograph. The column packing can be
any one of a number of solid supports coated
with a suitable silicone oil. Table 2.6 contains
a number of suggested GC columns. Section
6.3 contains information on open tubular
columns. Temperature programming should
be utilized with a relatively low initial
temperature to enhance resolution of more
volatile components, and a final temperature
that does not exceed the maximum operating
temperature of the column.
Inject an appropriate volume of extract into
the system with the ionizer off and either vent
the solvent or allow the solvent to be pumped
from the manifold. After about two minutes,
or when the pressure reaches 10"' torr, turn on
the ionizer, start data acquisition, and begin
temperature programming. Halt data
acquisition after about 40 minutes or until
peaks cease to appear. Either the control mode
or the IFSS mode may be utilized. The sample
dialogue below contains some suggested
operating parameters:
DELECT MODE: , CONTROL
CALIBRATE?: N_
TITLE: ANY TITLE UP TO 64
CHARACTERS
CALIBRATION FILE NAME: CURRENT
CALIBRATION FILE NAME
FILE NAME: UP TO SJX CHARACTERS
MASS RANGE: 40-450
INTEGRATION TIME: 8_
SAMPLES/AMU: J_
THRESHOLD: press return
RT ON CRT?: N_
RT GC ATTN: 1-8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 45
DELAY BETWEEN SCANS (SECS.)?:
press return
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: ANY TITLE UP TO 64
CHARACTERS
41
-------
CALIBRATION FILE NAME: CURRENT
FILE
FILE NAME: UP TO SIX CHARACTERS
MASS RANGE: 40-450
SAMPLES/AMU: J_
MAX RPT COUNT: 32
BASE INTEGRATION TIME: J_
RPT COUNT BEFORE CHECKING LOWER
THRESHOLD: 8_
LOWER THRESHOLD: 4_
UPPER THRESHOLD: 4_
RT ON CRT?: N^
RT GC ATTEN: 1-8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 45
DELAY BETWEEN SCANS (SECS.)?:
press return
EXTRACTION WITH A HIGH
BOILING SOLVENT
Extraction with a high boiling solvent is the
application of a relatively high molecular weight late
eluting solvent to the conventional liquid-liquid
extraction technique. This method has the advantage of
permitting the analysis of volatile compounds that are
usually lost during the concentration of a low boiling
solvent extract or masked by the solvent during gas
chromatography. The extraction is accomplished with
a relatively small volume of high boiling solvent and a
relatively large volume of water. The extract is
analyzed without further concentration, and no volatile
compounds are lost. The late eluting character of the
solvent permits data acquisition to begin immediately
after injection, and no volatile compounds are masked
by the solvent.
The scope of the high boiling solvent extraction
procedure is similar to inert gas purging and trapping.
However, high boiling solvent extraction has been
much less thoroughly evaluated. Very limited
information is available about the types of compounds
extracted with various high boiling solvents, detection
limits, or the precision and accuracy of concentration
measurements.
High boiling solvent extraction has the advantage
that no special equipment is required. Under these
circumstances the method should be of interest
primarily for rapid qualitative analysis.
A number of solvents appear suitable for this
application but hexadecane has been used most
frequently. Hexadecane is available commercially in
rather pure form, it is very insoluble in water, and it
elutes very late on many GC columns. Hexadecane
does have the disadvantage of low. polarity and is best
suited for the extraction of non-polar compounds and
mixtures such as aliphatic hydrocarbons, benzene,
toluene, the xylenes, gasoline, aviation jet fuel,
kerosene, carbontetrachloride, chloroform, and related
materials. The extraction efficiency will vary with
different classes of compounds and any concentration
measurements must be considered as minimum until
recoveries of spikes clearly establish the capabilities of
the method. The minimum detectable level for some
compounds is about 1 ug/1 when analyzing a 10 ml
extract of a one liter water sample. The extraction
efficiency has been found to be 85-95% for halogenated
methanes and aromatic hydrocarbons such as benzene,
toluene, and xylenes.
As always, reagent blanks must be employed to
establish that contamination is well controlled and the
precise level of contamination that is beyond control. It
should be verified by GC/MS that each batch of
hexadecane or another solvent is free of significant
quantities of interferring substances. Purify sodium
chloride and sodium sulfate by extraction with 50
volume per cent methylene chloride - acetone in a
soxhlet extractor for 8 hours. Air dry the solids and
heat in a 120C oven for 4 hours.
Samples are collected in one-liter, glass jars with
Teflon lined caps. Extracts are collected in 15 ml vials
with Teflon faced septa and aluminum crimp-on or
screw cap seals. This is required to prevent loss of
volatile compounds. Vials are available from the Pierce
Chemical Company, Box 117. Rockford, Illinois
61105. No other special equipment is required
Glassware for blanks, spikes, and samples should be
washed with detergent, rinsed with tap water, rinsed
with distilled water, thoroughly dried, and heated in a
muffle furnace for at least one hour at a minimum
temperature of 200C.
Add 10 ml of hexadecane to a one liter sample bottle
and collect about 950 ml of water sample. Cap the
bottle and shake vigorously. If the water temperature is
18C or below, the hexadecane will solidify. In this case,
wait until the hexadecane melts before shaking. Ship
the sample to the laboratory without refrigeration.
If phenols or other low molecular weight acids are of
interest, adjust the pH of the sample to 2 with
concentrated sulfuric acid. Shake the sample well and
transfer the contents to a 2 liter separatory funnel.
Shake vigorously for 2 minutes and allow the layers to
separate. If an emulsion occurs, add 5 grams of sodium
chloride, reshake, and allow the layers to separate.
42
-------
Drain off the water layer and measure its volume in a
1000 ml graduated cylinder. The added NaCl will not
increase the volume by a significant amount. Drain the
hexadecant- through a small filter funnel packed with
2 grams of anhydrous sodium sulfate over glass wool
into a 15 ml vial. Seal the vial by crimping on a Teflon
faced septum and an aluminum seal or use a screw-on
cap. The extract is now ready for GC/MS analysis.
Suggested gas chromatographic columns for high-
boiling solvent extract analysis are listed in Table 2.6.
Temperature programming from ambient to about
200C at 8 degrees per minute may be utilized. Begin
with GC oven door open to achieve an initial
temperature of about 50C. Turn on the ionizer, start
data acquisition, and then inject 2-8 microliters of
extract. Close the oven door and begin temperature
programming. Halt data acquisition before elution of
the hexadecane peak (generally about 10 minutes).
Either the control mode or the IFSS mode may be used
for data acquisition. The sample dialogue below
contains some suggested operating parameters:
SELECT MODE: CONTROL
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME: CURRENT FILE
FILE NAME: UP TO SIX CHARACTERS
MASS RANGE: 20-260 .
INTEGRATION TIME: 8_
SAMPLES/AMU: _1_
THRESHOLD: press return
RT ON CRT?: N_
RT GC ATTEN: 1-8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 20
DELAY BETWEEN SCANS (SECS.)?:
press return
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME: CURRENT FILE
FILE NAME: UP TO SIX CHARACTERS
MASS RANGE: 20-260
SAMPLES/AMU: j_
MAX RPT COUNT: 32
BASE INTEGRATION TIME: J_
RPT COUNT BEFORE CHECKING LOWER
THRESHOLD: 8_
LOWER THRESHOLD: 4
UPPER THRESHOLD: 4_
RT ON CRT?: N_
RT GC ATTEN: 1-8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 20
DELAY BETWEEN SCANS (SECS.)?:
press return
ADSORPTION WITH POROUS
POLYMERS
Adsorption with porous polymers is the application
of a solid phase, organic polymeric material to the
isolation and concentration of organic compounds in
water. The principal advantages of this technique are
the acquisition of time integrated (composite) samples
and the very low detection limits made possible by
sampling relatively large volumes of water..
In the past, activated carbon has been used
extensively as an adsorbent for organic compounds in
water. However the carbon adsorption method,
although still widely used, has a number of limitations.
High quality activated carbon is not always readily
available, significant effort is required to reduce
background, lengthy work-up procedures are required,
and many organic compounds are adsorbed so strongly
thatdesorption is accomplished in very low yield.
The porous polymer adsorption method has the
same advantages as the carbon adsorption method, but
fewer disadvantages. A variety of commercial polymers
are available, background contamination is more easily
removed, desorption does not require lengthy Soxhlet
extraction, and the recoveries in Table 3.5 are
acceptable for measurements of a wide variety of
compounds. These recoveries are based on elution with
diethyl ether and were selected from the literature cited
in section 10.3.
The porous polymers employed in this method are
called macroreticular resins. Macroreticular refers to
the relatively large, controlled pore size of the resin
beads. Each grain of resin is formed from many
microbeads that are cemented together during the
polymerization process. The pores are the spaces left
between the cemented microspheres.
The most-frequently used resins are the Amberlite
XAD series made by the Rohm and Haas Company.
They are hard insoluble beads of 20-50 mesh, varying
from white to light brown in color. Four materials are
available, XAD-2, 4, 7 and ». XAD-2 and XAD-4 are
styrene-divinylbenzene copolymers that are chemically
identical but differ in active surface area and average
43
-------
Table 3.5. Recoveries of Organics by Adsorption on Porous Polymers.
Compound Added XAD Resin Type %Recovery
Chlorinated Hydrocarbons
sym-tetrachloroethane
bis-chloroisopropyl ether
bromodichloromethane
dibromochloromethane
chlorobenzene
o-dichlorobenzene
m-dichlorobenzene
1,2,4,5-tetrachlorobenzene
1 ,2,4-trichlorobenzene
benzyl chloride
o-chlorobenzyl chloride
m-chlorotoluene
2,4-dichlorotoluene
p-chloronitrobenzene
Lindane
Aldrin
Dieldrin
Chlordane
DDT
DDE
Phenols
phenol
o-cresol
p_-cresol
3,5-xylenol
o-chlorophenol
g-chlorophenol
2,4,6-trichlorophenol
pentachlorophenol
1-naphthol
2, 4, 7, 8
2, 4, 7, 8
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2, 4, 7, 8
4
2, 4, 7, 8
4
4
4
4
2, 4, 7, 8
4
61, 72,
76, 80,
87
99
95
88
93
74
99
88
96
80
71
100
95
47
93
82
96
.81-
9
14, 40,
73
44, 69,
79
96
95
99
84, 84,
91
35, 59
76, 77
19, 29
33, 47
83, 77
Polycyclic Aromatic Hydrocarbons
naphthalene
1 -methylnaphthalene
2-methylnaphthalene
2-methoxynaphthalene
acenaphthene
biphenyl
fluorene
anthracene
tetrahydronaphthalene
dibenzofuran
diphenyl ether
2, 4, 7, 8
2, 4, 7, 8
2, 4, 7, 8
2
2, 4, 7, 8
2
2
2
2
2, 4, 7, 8
2
79, 80,
87, 77,
95, 77,
97
99, 81,
101
84
83
62
93, 82,
91
64, 78
64, 80
63, 77
72, 20
73, 95
44
-------
Table 3.5. Recoveries of Organics by Adsorption on Porous Polymers, (continued)
Compound Added XAD Resin Type % Recovery
Nitrogen Compounds
o^nitrotoluene 2, 4, 7, 8 82, 83, 53, 77
nitrobenzene 2 91
o-nitroaniline 2 100
hexadecylamine 2 94
indole 2 89
N-methylaniline 2 84
quinoline 2 84
isoquinoline 2 83
benzonitrile 2 88
Atrazine 2, 2 83, 100
benzothiazole 2, 4, 7, 8 100, 82, 40, 53
benzoxazole 2 92
Carboxylic Acids
octanoic acid 4 108
decanoic acid 4 90
palmitic, acid 4 101
oleic acid 4 100
benzoic acid 4 107
Alcohols
1-hexanol 2 93
2-octanol 2 100
1-decanol 2 91
benzyl alcohol 2 91
cinnamyl alcohol 2 85
2-phenoxyethanol 2 102
alpha terpineol 2, 4, 7, 8 81, 80, 36, 62
2-ethylhexanol 2, 4, 7, 8 99, 91, 74, 79
1-dodecanol 2 93
Aldehydes and Ketones
2,6-dimethyl-4-heptanone 2 93
2-undecanone 2 88
acetophenone 2 92
benzophenone 2 93
benzil 2 97
benzaldehyde *-' 2 101
salicylaldenyde 2 100
isophorone 2, 4, 7, 8 76, 86, 46, 47
45
-------
Table 3.5. Recoveries of Organics by Adsorption on Porous Polymers, (continued)
Compound Added XAD Resin Type % Recovery
Esters
benzyl acetate
di(methoxyethyl) phthalate
dimethyl phthalate
diethyl phthalate
dibutyl phthalate
di(2-ethylhexyl) phthalate
diethyl fumarate
dibutyl fumarate
di(2-ethylhexyl) fumarate
diethyl malonate
methyl benzoate
methyl decanoate
methyl octanoate
methyl palmitate
methyl salicylate
methyl methacrylate
Miscellaneous
n-hexadecane
ethylbenzene
cumene
g-cymene
dihexylether
dibenzylether
anisole
bromoform
iodobenzene
pore diameter. XAD-2 has 300 mVg active surface
area and 90 A average pore diameter compared to
784 mVg and 50A for XAD-4. XAD-7 and XAD-8
are both acrylate polymers having active surface areas
of 7 50 mVgand!40 mVg and average pore diameters
of 80 A and 250 A, respectively. The resins derive
their adsorptive properties from their macroreticular
porosity, pore size distribution, and high surface area.
XAD's 2, 4, and 7 are available from Mallinckrodt
distributors such as Curtin. All four are available from
Chemical Dynamics Corp., Hadley Road, P.O. Box
395, South Plainfield, New Jersey 07080.
In practice, water is passed through a column of
XAD resin and the organic materials are adsorbed. The
organics are desorbed from the resin by elution with an
organic solvent and the extract is submitted to GC/MS
2, 4, 7,
2
2
2
2
2
2
2
i
100
94
91
92
99
88
86
92
84
103
101
95
98
70
96
35
3, 11, 3, 18
81
93
92
75
99
87
101
81
analysis. A number of elution solvents have been
evaluated and methylene chloride and acetone are very
effective. Diethyl ether and chloroform are not
acceptable for the reasons discussed in the low boiling
solvent extraction method.
The method has been applied to a wide variety of
organic compounds and is applicable to non-ionized
materials having boiling points above about 100C. The
detection limit is of the order of 1-10 ng/1 in an
aqueous matrix. In general, overall recoveries are
equivalent to those obtained with low boiling solvent
extraction. Table 3.5 contains a number of values that
have been reported using diethyl ether for elution. For
accurate concentration measurements, these recoveries
must be established in the laboratory conducting the
procedure.
46
-------
As in other methods, a reagent blank is required to
assure that compounds detected are not contaminants
of the glassware or materials. The reagent blank may
consist of one liter of low organic water.
Reagents and Equipment. Extract glass wool in a
Soxhlet apparatus with methylene chloride before use.
Methartol, methylene chloride, and acetone should be
of high quality and redistilled before use in all-glass
apparatus. (See the low boiling solvent extraction
method for precautions in the use of these solvents).
Sodium sulfate should be extracted and dried before
use.
Low organic water is prepared by passing tap water
through a filtration system consisting of cation and
anion-exchange columns and activated carbon
columns. This water is then distilled in an all-glass
apparatus. The resulting deionized/distilled water is
then passed through an XAD-2 column as a final clean-
up step.
Some special equipment is required for this method.
The resin columns are custom made from liquid
chromatography columns, 25 mm O.D., 22 mm I.D.,
equipped with a Teflon stopcock. The columns are
shortened to about 180 mm (packing length) and fitted
with 24/40 female joints at the top of the column. The
column also should have glass "ears" near the top for
securing the glass stoppers or the glass adapters with
rubber bands or wire springs. Other arrangements are
also acceptable; the main requirement is that the ratio
of length to inside diameter should be about 7. The
stoppers are 24/40 ground glass stoppers equipped
with glass "ears".
For automatic continuous sampling, a variable speed
peristaltic pump capable of pumping at a rate of
120 ml/min is used. The pump is attached to the
stopcock end of the column with Tygon tubing. The
water sample is drawn through the column from the
other end using an adapter and Teflon tubing. The
recommended flow rate is four bed volumes per minute.
Adapters are required to connect the column with
1/4 inch O.D.Teflon tubing that is placed in the sample
source. The adapter consists of a 24/40 male joint
joined to a short section of 1/4 O.D. glass tubing. The
glass tubing is connected to the Teflon tubing by a brass
Swagelok adapter fitted with Teflon ferrules. The glass
adapter is equipped with glass "ears" for securing in
place rubber bands or wire springs.
Kuderna-Danish equipment is required for the final
concentration of the eluate. (See the low boiling solvent
extraction procedure for a list of this equipment).
Procedure. The commercial XAD resins are
contaminated. Preextraction to remove interferring
impurities is required.
1. Slurry the desired amount of resin in methanol
and decant to remove the fine particles. Place
the resin in a Soxhlet apparatus of appropriate
size using glass wool plugs to hold the resin in
place.
2. Extract the resin sequentially with acetone,
methanol, and methylene chloride utilizing a
minimum often cycles per solvent.
3. With the resin still in the Soxhlet apparatus,
rinse three times with methanol. Store the
resin in a closed glass container under
methanol. Do not allow to dry.
An alternative cleanup procedure uses
extraction with acetone and acetonitrile,
followed by vacuum degassing at 200C and
10"* to 10"' torr. If a large Soxhlet is not
available, 100 g batches can be cleaned up by
placing them in a 5 cm I.D. column and
washing successively with two liters of
acetone, methanol, and methylene chloride.
Concentrate a portion of the methylene
chloride effluent, and check it for background.
Repeat the methylene chloride wash if
necessary. Remove the resin from the column
and store under methanol.:
4. Plug the bottom of the resin column with
1-2 cm of pre-extracted glass wool. Add the
XAD resiri to the column as a methanol slurry.
Adjust the resin height in the column to about
8 cm. Stir with a glass rod to remove any
trapped air. Plug the top of the column with
1-2 cm of glass wool. Do not allow the column
to dry.
5. Add 30 ml of low organic water, let drain until
water reaches the top of the glass wool. Repeat
three times.
6. The column is now ready for a sample. If
stored or shipped, the column should be filled
with water and stoppered such that all air
pockets are excluded.
7. Grab samples generally consist of 1 to 5 liters
of water. It may be desirable to adjust the pH
of the sample prior to passing it through the
column. For example, the recovery efficiencies
for phenols and carboxylic acids are greater
when performed at lower pH. Pass the water
through columns by gravity at a flow rate of
approximately four bed volumes per minute
47
-------
(ca. 120 ml/min.)- Any sample except drinking
water may contain suspended matter that is
trapped on the glass wool and reduces the flow.
In this case a peristaltic pump at the bottom of
the column for samples greater than 1 liter is
suggested. Allow sample to drain freely and
close the stopcock. If the column is to be stored
or shipped prior to solvent extraction, fill with
organic free water, exclude air bubbles, and
stopper. Frequently air bubbles form in the
column during the adsorption step; ignore
them.
8. 'For composite samples, the columns can be
.used for manual compositing. For example, in
the field, one liter of effluent water can be
passed through the column every hour over the
desired sampling period (8-24 hours) as a time
composite. Composites can,also be taken by
attaching the column to a peristaltic pump
having the appropriate pumping speed (ca. 120
ml/min or less). The water to be sampled is
drawn to the column through Teflon tubing
(1/4 inch O.D.). The effluent end of the
column is attached to the peristaltic pump
with Tygon tubing. The flow rate should be
checked periodically to determine the volume
sampled.
9. For.desorption, allow the column to drain
freely. Close the stopcock and place a 300 ml
Erlenmeyer flask under the column.
10. Add 30 ml of acetone and force the solvent
through the resin at a slow rate (dropwise)
using nitrogen pressure (ca. 2 p.s.i.) if
necessary.
11. Allow the acetone to drain until it is just to the
top of the upper glass wool plug.
12. Repeat steps 10 and 11.
13. Continue desorption with eight bed volumes of
methylene chloride.
14. Remove the water layer from the eluate using a
disposable glass pipette.
15. Dry the eluate with organic-free anhydrous
sodium sulfate, and concentrate by Kuderna-
Danish evaporation to a volume of about 5 ml.
The volume can be further reduced over a
warm water bath by directing a stream of clean
air or nitrogen onto the extract. (See the low
boiling solvent extraction procedure for
cautions during concentration). The extract is
now ready for GC/MS analysis.
16. Often the resin columns can be reused after a
minimum amount of cleanup. However, if the
sample was extremely dirty and contained
sediment, it-is recommended that the resin be
discarded. If the r'esin is discolored, replace the
upper glass wool plug. Add 30 ml of acetone
and allow to drain freely. Repeat the acetone
wash twice. Add 30 ml of organic free water
and .allow to drain freely. Repeat the water
wash twice. The column is now ready to reuse.
The GC/MS conditions are the same as
given under the low boiling solvent extraction
procedure. Suggested columns are in
Table 2.6.
3.2 All SAMPLES
Air sampling and analysis methods have been under
development for many years, and numerous methods
are available for the isolation, concentration, and
measurement of specific organic compounds in air
samples. However, as emphasized in chapter one, the
purpose of this manual is to describe broad spectrum
methods for general classes of organics. In this area
there is relatively little information available.
Therefore, the methods given in this section probably
represent the first generation broad spectrum air
procedures, and significant improvements will
probably occur in future years.
The problem of quantitative sampling of air is
significantly more complex than is quantitative
sampling of water. Numerous studies of the sampling
problem have been conducted and the results reported.
It is beyond the scope of this manual to reproduce the
detailed methodology required for accurate
quantitative sampling of organics in air. The broad
spectrum methods described in this chapter are most
appropriate for qualitative or rough quantitative
analyses of air samples.
After sampling and the initial sample preparation,
the GC/MS aspects of air analyses are not unlike the
analyses of samples from other media. Therefore, a
great deal of information from the other sections of this
chapter and other chapters is applicable to air analyses.
Numerous references to these sections are made under
Air Samples.
DIRECT AIR INJECTION
Direct air injection is the introducion of a few ml,
e.g., 5, of air into the GC/MS system. This procedure is
clearly similar to the qualitative headspace analysis
described in section 3.1. The advantage of this method
48
-------
is the speed of the analysis and relative simplicity of
sample handling. The disadvantage is that the method
is limited to relatively high concentrations of volatile
compounds such as vinyl chloride or chlorotrifluroro-
methane. The detection limit is estimated to be about
two milligrams .per cubic meter (kiloliter) of air. This
procedure will probably be useful only for an industrial
work site or a spill site. Generally ambient air levels of
organics are in range of tens of picograms to nanograms
per cubic meter. Industrial work rooms or source
effluents usually do not exceed tens of micrograms per
cubic meter, but many exceptions are possible and have
been reported. The application of selected ion .
monitoring as described in section 6.1 may lower the
detection limit of the method to the microgram per
cubic meter level.
For this procedure glass collecting tubes of 100-500
ml capacity fitted with gas tight stopcocks and rubber
septa are evacuated in the laboratory. The stopcock is
opened at the sampling site, and sampling is continued
until the pressure in the collecting tube is equivalent to
the external pressure. The stopcock is closed and the
container is returned to the laboratory. An aliquot of
the sample is removed with a gas tight syringe and
injected directly into the GC/MC system Sampling
containers are commonly available from general
laboratory supply companies.
The GC columns suggested for direct, aqueous
injection in Table 2.7 are also recommended for direct
air injection. Initial column temperature should be as
near ambient as possible. A holding time of several
minutes is suggested followed by temperature
programming at 4-8 C/min. A sample run time of
about 30 min. is usually sufficient. Suggested sample
data acquisition parameters are as follows:
SELECT MODE: CONT
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME: CURRENT FILE
FILE NAME: UP TO 6 CHARACTERS
MASS RANGE: 14-16;19-27;29-31;
33-260
INTEGRATION TIME: 17;17;17;17
SAMPLES/AMU: 1;1;1;1
THRESHOLD: press return
RT ON CRT?: N_
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: UP TO 64 . CHARACTERS
CALIBRATION FILE NAME: CURRENT
FILE
UP TO 6 CHARACTERS
14-1=3; 19-27:29-31;
FILE NAME:
MASS RANGE:
33-260
SAMPLES?AMU: 1; 1; 1; 1
MAX RPT COUNT: 32
BASE INTEGRATION TIME: J_
RPT BEFORE CHECKING LOWER
THRESHOLD: 8_
LOWER THRESHOLD: 4_
UPPER THRESHOLD: J_
RT ON CRT?: N_
RT GC ATTEN 1 - 8
FAST SCAN OPT?: N_
MS-RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
ADSORPTION WITH POROUS POLYMERS
This method involves passing a measured amount of
air through a solid adsorbent, followed by thermal
desorption of organics into the GC/MS system. The
advantage of this method compared to cryogenic
trapping is the significantly simpler field equipment
handling. The advantage, compared to solvent
desorption, is higher sensitivity because the total
sample is measured and there is no background from
the solvent. The principal disadvantage is that because
the total sample is measured, there is no room for error
in the analytical procedure. Multiple samples should be
collected to provide the required back-up in the event
of a laboratory accident or equipment malfunction, and
to obtain information on the precision of the method.
The porous polymer adsorption method is applicable to
organics having compositions in the C6 to CIS range.
Although several different adsorbents have been
used by various researchers, Tenax GC appears to have
several advantages over the others. This material is
thermally stable to about 350C, has good adsorption
characteristics, but does not efficiently retain water
vapor. However caution must be excercised because
some batches of Tenax have been reported to
decompose at lower temperatures. Detection limits are
not well established for these methods, but probably are
about 1-10 ug per cubic meter"(kiloliter) of air. Good
quality control requires that unused adsorbent be
desorbed at frequent intervals with the identical
49
-------
conditions used with the samples. This will assure that
background contamination from the adsorbent itself or
from the equipment is under control, or, at least, is
known to the investigator. There is limited recovery
data available for this method.
Tenax GC (2,6-dlphenyl-p-phenyleneoxide polymer)
is available from several suppliers including. Applied
Science, State College, Pennsylvania. This must be
purified before use by extracting with methanol for
several or more hours in a Soxhlet apparatus.
Purification may not be necessary if purified material is
available from the supplier, but the material is
susceptible to decay and contamination during storage.
The Tenax GC, 60/80 mesh adsorbent is packed into
Pyrex glass tubes of 2.5 mm I.D. x 200 mm dimensions.
The adsorbent is supported by 0.5 cm plugs of silanized
glass wool. Prior to use the tubes and glass wool may be
heated to 500 C for several hours to remove traces of
organic matter. The packed sampling tubes are
conditioned at 270 - 300 C for 0.5 - 1 hour under a
helium or nitrogen flow of 30 - 50 ml/min. After
cooling to room temperature, cap both ends or store the
sampling tube in a clean screwcapped test tube.
Sampling pumps are available from several
laboratory supply companies. A flowmeter should be
precalibrated with a sample tube connected using a
soap bubble^ flowmcter. The sample is taken by pulling
air through the tube at a rate of about 500 ml/min.
After a suitable sampling period of 2 - 4 hours in urban
locations, the pump is turned off, and the tube is capped
or stored until the analysis can be performed.
The sample is analyzed by direct heat desorption at
250 - 270 C for three minutes under a 10 ml helium
flow. A desorption technique similar to that described
under inert gas purging and trapping is recommended.
The GC column oven is reduced to ambient
temperature before desorption begins, then
programmed to an elevated temperature at 4 - 8/min.
The columns described in Table 2.6 for solvent extracts
are recommended for porous polymer trapped samples.
Data collection should begin just prior to the
desorption step. The following GC/MS operating
conditions are recommended for the control and IFSS
modes.
SYSTEM 1500 IS ON SELECT MODE:
CONT
CALIBRATE?: . N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME: CURRENT FILE
FILE NAME: UP TO 6_4 CHARACTERS
MASS RANGE: 14-16;19-27;29-31;
33-260
INTEGRATION TIM'E: 17;1 7;1 7; 17
SAMPLES/AMU: 1;1;1;1
THRESHOLD: press return
RT ON CRT?: N_
RT GC ATTEN: 1 - 8 .
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: UP TO 64 CHARACTERS
CALIBRATION FILE NAME: CURRENT
FILE
FILE NAME: UP TO 6 CHARACTERS
MASS RANGE: 14-16;19-27;29-31;
33-260
SAMPLES/AMU: 1;1;1;1
MAX RPT COUNT: 32 BASE
INTEGRATION TIME: J_
RPT BEFORE CHECKING LOWER
THRESHOLD: 8_
LOWER THRESHOLD: 4_
UPPER THRESHOLD: j_
RT ON CRT?: N_
RT GC ATTEN: 1 - 8
FAST SCAN OPT?: N_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?:
press return
FILTRATION WITH GLASS FIBER
FILTERS
This method is for the analysis of organic
compounds contained in paniculate matter (dirt, dust,
etc.) collected from air with a glass fiber filter.
Paniculate matter itself is a criteria pollutant that is
known to be rich in organic material. The advantage of
this method is that it specifically addresses the problem
of organics in particulate matter. The disadvantage is
that gas phase, low molecular weight organics are not
adsorbed on glass fibers. In this method air is drawn
into a covered housing and through a glass fiber filter
by means of high flow rate blower (HI VOL sampler),
the mass of the collected particulate matter is
determined, the organics are removed by Soxhlet
50
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extraction, and analyzed by GC/MS. The extract may
be separated with silica gel into aliphatic, aromatic, and
oxygenated fractions prior to GC/MS analysis.
Generally, for urban particulates, alkanes ranging from
C,,H36 to Cj,H6J will be found in the aliphatic fraction,
compounds such as anthracene, pyrene, and
benzopyrene will be found in the aromatic fraction, and
phenols, phthalate esters and other polar compounds
will be found in the oxygenated fraction.
Methylene chloride is the solvent of choice for
general purpose work. The reasons for choosing
methylene chloride are exactly the same as given under
the low boiling solvent extraction method in section 3.1
of this chapter. The specifications for glass fiber filters
and the detailed procedure for use of a HI VOL
sampler are beyond the scope of this manual, but are
well documented in other publications. The user should
see the Federal Registered, 8186 (1971). Additional
information is available from the director of the
Environmental Monitoring and Support Laboratory,
Research Triangle Park, North Carolina.
The detection limit for this method is not well
established, but is probably about one ng per kiloliter
(cubic meter) of air. Typically a 24 hour sample of 2500
kl in an urban location will yield 125 - 150 mg of
paniculate matter (60 - 200 ug/kl) of which about
10% is extractable. It is absolutely essential that an
unused glass filter from the same batch of filters be
extracted at the same time and under the same
conditions as the loaded filters. The analysis of this
unused filter will provide information about
background and solvent contamination. There are no
recovery data available for this method.
The methylene chloride should be distilled as
described under low boiling solvent extraction
immediately before use. The weighed filter is cut into
pieces small enough to fit into a 250 ml Soxhlet
extractor. Usually only one section of the whole filter is
used for the organics analysis. No thimble should be
used, but about one inch of pre-extracted glass wool is
placed in the bottom of the extraction chamber. This
will act as a filter and preclude the accumulation of
paniculate matter in the distillation pot. The filter
pieces are inserted, and 200 ml of solvent is placed in
the pot. Extraction should continue for 25 cycles, and
the cooled extract transferred to a Kuderna-Danish
(K-D) apparatus. If the optional silica gel separation is
to be used, concentrate the extract to 1 ml; if no silica
gel separation is planned, concentrate to 0.1 - 1 ml.
For the silica gel separation, pack activated silica gel
into a glass chromatography column (2 cm I.D.) to a
height of 10 cm. To the 1 ml of extract in a small
beaker add sufficient silica gel to adsorb the sample,
and then evaporate the residual solvent with gentle
stirring in a hood. Wet the column with about 20 m 1 of
hexane and add the sample when the last of the 20 m 1
reaches the surface of the adsorbent. Rinse the beaker
with hexane and add the rinsings to the column. The
beaker should be rinsed several times with hexane and
each succeeding eluent when the eluent is added to the
column. Collect the fractions in K-D ampuls and elute
the aliphatic fraction with 85 ml of hexane, the
aromatic fraction with 85 ml of.benzene or the safer
toluene, and the polar fraction'with 1:1 methanol-
methylene chloride. Concentrate each fraction to 0.1 -
1 ml in the K-D apparatus, and proceed with the
GC/MS analysis of each.
The GC columns and conditions recommended are
the same as those used for low boiling solvent
extraction. This procedure should be consulted for this
information. Also see the previous section for sample
GC/MS system dialogue.
3.3 SEDIMENT SAMPLES
Sediment is defined as wet solids taken from the
bottom of a stream, river or lake. This method is
applicable to these, and with the elimination of the
drying step, to the broad spectrum analyses of organics
in dry soils and related matter. In the method a
sediment sample is partially dried and extracted in an-
ultrasonic homogenizer (e.g., a Polytron) with a 1:1
mixture of acetone-hexane. The residue is filtered and
the extract concentrated in a Kuderna-Danish (K-D)
apparatus. The concentrated extract may be analyzed
directly by GC/MS or optionally separated into
fractions with activated silica gel. The purpose of the
acetone solvent is to provide a water-soluble wetting
agent to stimulate desorption of organics from the solid
material in the sample. The advantage of this method is
that it uses a reasonably well tested extraction
procedure and a familiar, well established optional
preliminary fractionation scheme. The detection limit
is not known, but is estimated at about 1-10 ug per kg
of dry solids. Quality control must include a single
reagent blank for each group of samples extracted on a
given day. A reagent blank is the result of processing
through the entire method all the same quantities of
materials and labware, except that the sediment itself is
not included. The result of the reagent blank analysis
documents the background and reagent contamination.
It is not possible to determine recoveries with this
51
-------
method since it is not possible to spike a sediment and
simulate natural adsorption conditions. One method of
estimating the degree of desorption is to re-extract the
processed sediment with fresh solvent or a second
solvent pair such as methylene chloride-acetone, and
determine if additional amounts of the same compound
are obtained.
Purify the reagents and solvents as described under
low boiling solvent extractions in section 3.1. Standard
laboratory glassware and equipment is required for this
method. See the equipment section under low boiling
solvent extractions in section 3.1. The ultrasonic
homogenizer recommended is a Polytron model PT-
20ST, Brinkmann Instruments, or the equivalent.
There also are a number of ultrasonic tissue
homogenizers available and these are reported to give
good results. A stainless steel container is
recommended for blending to preclude breakage by
stones or other hard objects.
Decant and discard the water layer over the
sediment, and mix the residue to obtain as
homogeneous a sample as possible. Transfer the sample
to a shallow pan to partially air dry for about three days
at ambient temperature. It is a good idea to select and
remove from the sample large debris such as stones,
broken glass, and bottle caps. Drying time varies
considerably depending on soil type and drying
conditions. Sandy soil will be sufficiently dry when the
surface starts to split, but there should be no completely
dry spots. Moisture content will be 50-80% at this
point.
Weigh 50 g of the partially dried sample into a 600
ml stainless steel beaker. Add 50 g of anhydrous
sodium sulfate and mix well with a large spatula.
Immediately after weighing the sample, weigh
approximately 5 g of the partially dried sediment into a
tared crucible. Determine the percent solids by drying
overnight at HOC. Allow the crucible to cool in a
desiccator before weighing. Optionally one may
determine the percent volatile solids by placing the
oven dried sample into a muffle furnace and heating at
550C for one hour. Again the crucible should be cooled
in a desiccator before weighing. The concentrations of
organic compounds are normally expressed as the
percent of the dry solid after the 1 IOC treatment.
To the 50 g sample add 250 ml of 1:1 acetone-
hexane, lower the homogenizer into the beaker until it
is approximately one cm from the bottom. Tilt the
probe slightly about 15 degrees' from vertical to prevent
the solution from swirling out of the chamber while
blending. Blend at maximum speed for 30 seconds.
Raise the probe out of the solution and rinse it with
acetone, allowing the rinsings to drain into the beaker.
Filter the homogenized mixture through a 7 cm or
larger medium porosity fritted glass funnel into a K-D
flask fitted with a 10 ml ampul. Rinse the beaker with
acetone and wash the filter cake with the rinse acetone.
Clean the probe between samples with successive 15
second runs in tap water, distilled water and acetone.
Wipe off the residual solid material between cleaning
runs.
If the optional silica gel separation is to be used,
concentrate the extract to 1 ml; if no silica gel
separation is planned, concentrate to 0.1-1 ml as
described under low boiling solvent extraction in
section 3.1.
For the silica gel separation, pack activated silica gel
into a glass chromatography column (2 cm I.D.) to a
height of 10 cm. To the 1 ml of extract in a small
beaker add sufficient silica gel to adsorb the sample,
and then evaporate the residual solvent with gentle
stirring in a hood. Wet the column with about 20 m 1 of
hexane and add the sample when the last of the 20 m 1
reaches the surface of the adsorbent. Rinse the beaker
with hexane and add the rinsings to the column. The
beaker should be rinsed several times with hexane and
each succeeding eluent when the eluent is added to the
column. Collect the fractions in K-D ampuls and elute
the aliphatic fraction with 85 ml of hexane, the
aromatic fraction with 85 ml of benzene or the safer
toluene, and the polar fraction with 1:1 methanol-
methylene chloride. Concentrate each fraction to 0.1-1
ml in the K-D apparatus, and proceed with the
GC/MS analysis of each.
The GC columns and conditions recommended are
the same as those used for low boiling solvent
extraction. This procedure should be consulted for this
information. Also see section 3.1 for sample GC/MS
system dialogue.
3.4 FATTY TISSUE SAMPLES
This method is intended for the extraction of a broad
spectrum of environmentally significant organics from
fatty tissue, and the separation of these organics from
the natural fats and oils prior to GC/MS analysis. The
method has been tested mainly with fish tissue, but
should be applicable to other types of tissues. The
analysis of fish tissue is used to describe the method,
with optional sample handling for the analysis of the
whole fish, or just the potentially edible portions. The
advantage of the method is that it is based on a
significant amount of experience of several
52
-------
investigators over a number of years. The detection
limit for the method is not known, but is estimated at
1-10 ug per kg of fish tissue.
The analysis of a reagent blank is required for each
group of fish specimens extracted on a given day. The
reagent blank analysis provides information about
background and solvent contamination. Recovery data
are not available for the total procedure since it is not
possible to spike fatty tissue with known concentrations
of organics and simulate natural conditions for the
incorporation of these materials. Perhaps the best
method of measuring the effectiveness of the extraction
is to re-extract with a fresh portion of solvent, or with
an alternative solvent, such as acetone-methylene
chloride.
Solvents and other reagents should be purified as
described under low boiling solvent extraction in
section 3.1. For the analysis of large whole fish, a meat
. grinder is required. In all cases, a laboratory blender of
about one quart capacity is also required. A gel
permeation chromatograph equipped with a 2.5 x 50
cm column packed with BIO-RAD SX-2 beads is used
to separate the natural fats and oils from the organics of
interest.
Fish at the sampling site should be wrapped in
aluminum foil, shipped in an ice chest packed with dry
ice (preferred) or ice, and preserved in a freezer until
analyzed. Small fish must be combined by sampling site
and species to obtain the weight required for analysis.
For the analysis of whole fish, the entire fish (or fishes)
are ground directly, or, if necessary, chopped into
pieces small enough to fit into the meat grinder. Grind
the fish several times and thoroughly mix the ground
material. Clean out any material remaining in the
grinder and add this to the sample. For an analysis of
the edible portions only, fillet the fish or fishes, and cut
these into small pieces no larger than about two cubic
centimeters each.
Add enough dry ice to the blender to completely
cover the blades. Homogenize the dry ice for about 30
seconds, and then add about 25 g (weighed to the
nearest 0. Ig) of fish fillet chunks or ground whole fish
along with more dry ice to the blender: Wait several
minutes for the fish to freeze, homogenize for at least
two minutes, or until the mixture is free of lumps, and
then add about 75 g of purified anhydrous sodium
sulfate to the blender. Homogenize for another two
minutes, and pour the contents of the blender onto an
aluminum foil sheet (one square foot). Homogenize
additional dry ice and 25 g of anhydrous sodium sulfate
and transfer this to the same aluminum foil. This
operation serves to rinse the blender of residual fish
residue. Mix the fish, sodium sulfate, and dry ice on the
foil with a spatula. Carefully fold the aluminum foil
into the form of an envelope, label, and place in a
freezer at -15C for 8-12 hours. The dry ice will
sublime and the residue should be in the form of a
granular lump-free material.
Extract the mixture in a 250 ml Soxhlet extractor
with 200 ml of a 1:1 mixture of acetone-hexane for 8
hours. Cool the extract, transfer it to a Kuderna-
Danish (K-D) apparatus, and concentrate it to about 3
ml. Remove the last traces of solvent with a gentle
stream of dry nitrogen, and weigh the resulting oil.
Dilute the oil with methylene chloride to a
concentration of 100 mg/m 1.
. Inject the total amount of diluted extract, in 5 m 1
aliquots, into the gel permeation chromatographic
system. Elute each 5 mlx aliquot with 225 ml of
methylene chloride, at a flow rate of 3.5 m 1 per minute,
and discard the first 160 ml of each eluate (this
contains the natural oils and fats). Collect the balance
(about 65 ml) of each eluate from each aliquot in the
same 500 ml K-D flask. Concentrate the combined
eluate containing the organics of interst to 5 ml.
Equilibrate the gel permeation system with a 1:1
mixture of cyclohexane-methylene chloride. Inject the
5 ml of concentrated combined eluate and elute with
300 ml of 1:1 cyclohexanemethylene chloride at 3.5 ml
per minute: Again discard the first 160 ml which
contains the residual lipid material. The remaining
. eluate may be divided into 3-10 fractions or collected
as a single fraction. Concentrate each fraction to 0.1 - 1
ml in a K-D apparatus as described under low boiling
solvent extraction in section 3.1. The GC columns and
GC/MS conditions used for the low boiling solvent
extraction procedure are recommended for this
method.
3.5 CHEMICAL DERIVATIZATION
OPTIONS
Chemical derivatization methods have been
developed extensively since 1955. Much of this effort
was directed toward functional goup selective reagents
for derivatization of specific target compounds or
narrow classes of compounds; e. g., steroidal alcohols.
In terms of the broad spectrum approach defined in
chapter 1 of this manual, a few reasonably general
reagents, such as diazomethane, have been employed
for derivatization . of several broad classes of
compounds, e. g., phenols, fatty acids, etc., that
generally appear in the acid fraction of a low boiling
53
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solvent extract. Historically, derivatization procedures
were needed to allow the gas chromatographic
separation of compounds that were difficult or
impossible to handle with existing liquid phases and
solid supports. However, there has been a steady
improvement in packing'materials and open tubular
column technology, and several classes of compounds,
such as the steroids, phenols, and fatty acids, may now
be conveniently chromatographed without
derivatization. Under these circumstances, serious
consideration must be given to the derivatization
option, and the need for this additional step in any
broad spectrum organic analysis. The advantages and
disadvantages of derivatization are summarized in this
section.
A clear advantage of chemical derivatization is that
several or many different classes of compounds may be
readily chromatographed with a few general purpose
columns. Without derivatization, it may be necessary
to change columns frequently to accomodate certain
classes of compounds, e. g., phenols and fatty acids.
Another advantage of derivatization is that atoms may
be introduced into various compounds that give the
compounds special properties that aid in their
identification. Examples of this include the
incorporation of a high fraction of heavy atoms such as
deuterium or carbon-13, and naturally occurring
isotope distributions, such as bromine-79 and bromine-
81.
The disadvantages of derivatization include the
additional cost, mainly in time and reagents, of these
procedures. On the surface, the additional costs may
appear slight, but additional quality controls will be
required, .and these may double or triple the number of
GC injections which are time consuming and produce
significantly more data that needs to be stored and
interpreted. The real question is whether the additional
cost is worth the additional information that may be
acquired. Another disadvantage is the uncertainty
about yield in any derivatization procedure. Unless
adequate control samples are derivatized
simultaneously under identical conditions with
identical reagents, the measurement accuracy of the
method may be seriously affected. Independent of the
use of quality control samples, derivatization for broad
spectrum organics analysis creates considerable
uncertainty with regard to what the reagents are doing
to many other components of the mixture. By-products
and side reactions are not uncommon, and commercial
reagents are frequently impure and introduce trace
impurities that could be mistaken for sample
components. The problems of reagent shelf life and the
frequent poisonous and explosive nature of many
reagents, e.g., diazomethane, are disadvantages that
need to be carefully weighed in the cost-benefit
equation.
In conclusion, it is recommended that for most broad
spectrum analyses derivatization is not worth the
effort, and that column switching is preferable.
However, if certain target compounds, e. g., 2,4,6-
trichlorophenoxyacetic acid, must be included in the
analysis, derivatization is the only practical choice at
this time. In the future, liquid chromatography - mass
spectrometry interfaces may be developed to an extent
to permit direct analysis of some classes of compounds
not readily chromatographed without derivatization.
If it is necessary to form a derivative of a specific
target compound, the commercially available reagents
and procedures are strongly recommended. The Pierce
Chemical Company of Rockford, Illinois, has been
particularly active in developing these reagents, and a
detailed discussion of the merits of various materials
and procedures is beyond the scope of this manual. The
choice of a reagent and procedure depends on the target
compound or compounds, and usually several reagents
and procedures will be available. Some important
considerations in selecting procedures are the speed of
the reaction, the convenience of the procedure, side
reactions, and reproducibility. Often very pure and dry
reagents are required, including generally anhydrous
conditions. The commercially available reaction vials
with Teflon lined septum tops are strongly
recommended.
Finally, because of its particularly hazardous nature,
a word about diazomethane is appropriate. It is a
highly poisonous and very explosive yellow gas.
Extreme caution must be exercised to avoid inhaling it
or allowing it too near an open flame. The diazotization
reaction must be conducted in an effective fume hood
and safety glasses and shields are mandatory. No
chipped, etched, or cracked glassware can be used
because rough glass surfaces enhance the
decomposition of diazomethane.
54
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CHAPTER 4
DATA OUTPUT
The purpose of this chapter is to provide the
information that is needed to output data with a
computerized gas chromatography-mass spectrometer
system. The chapter describes in detail the operation of
programs that run on a Digital Equipment Corporation
Model PDP-8 Computer.
One of the most fundamental and important
programs that the user of a system requires is one that
types out a list of programs and data files. All computer
acquired data and all computer programs are stored as
named files on either the disk or tape storage device.
The names of the data files currently existing on the
disk are required before output can begin. Only the files
on the disk can be directly output when a disk
operating system is in use. Output directly from tape is
possible only with a tape operating system. If a disk
operating system is in use, and output is required from
magnetic tape, the file must first be copied from tape to
disk before output can begin. (See the copy program in
Chapter 7).
There are a number of programs available to list the
programs and data files on a disk or tape. Each or these
programs is somewhat different in hardware
requirements, and user input. Only three of these
programs are described in this section, and only three
are supported under the revision EO operating system.
The program names and hardware requirements are as
follows:
Program
Name
LIST
LIST
MAGLST
BCLIST
LSTDSK
LSTBLK
LSTDAT
Status
Unsupported
Supported
Supported
Unsupported
Supported
Unsupported
Unsupported
Sample dialogue for the supported
as follows:
Hardware
Disk unit 0 and TC08
Dectape unit !
Disk unit 0 and TD8E
Dectape unit 0
9-track industry standard
magnetic tape
Disk units 0 or 1
and TC08 Dectape units 0-7
Disk units 0-3 and
TC08 Dectape units 0-7
Disk unit 0 only
Disk unit 0 only
LIST program is
55
-------
SELECT MODE: LIST
TAPE?: N_
NAME BLOCK
INIT$$
EXEC
EXMODI
CUEXEC
ETC.
15
17
47
76
In the dialogue a Y_to the TAPE prompt causes the
files on TD8E Dectape unit 0 to be listed. An entry of
LIST to the system prompt and M to the TAPE
prompt calls the program MAGLST which causes the
files on the industry standard tape to be listed.
For users with TC08 Dectapes or users who wish to
list the files on disk units 1-3, the program LSTDSK
replaces the TC08 LIST program and BCLIST.
LSTDSK requires 8 K of core memory and an
extended arithmetic unit. The only input required is the
disk number DO, Dl, D2, or D3 or the TC08 Dectape
number TO-T7.
4.1 THE OUTP/CRT SOFTWARE
The plotter and printer programs that are called by
entering OUTP in response to the system prompt are
the original output programs for the PDP-8 GC/MS
datasystem. As such, they are relatively simple
programs that require only 4K of memory and no
special PDP-8 hardware. Nevertheless, they have some
capabilities not available in the output software
described under sections 4.2 and 4.3. Also, they are
programs that are easy to use by the relatively
inexperienced user. For these reasons they have been
retained on the system, and are used extensively in
many laboratories. Eight files are required on the
system disk to run these programs: EXMODI,
PLOUT, PLOT, PLTP2, CUEXEC, RGC, TYPE, and
BACKGD. These programs handle output from disk
unit 0 only. Another program, PERCAL, may be used
to retrieve stored operating parameters from any stored
data file. This program is explained in more detail in
section 2.7.
The CRT program requires 8K of memory and the
files CRT, CRTRGC, CRTSP, CBCKGD, and
DSPLAY must be present. ,
THE TOTAL ION CURRENT PROFILE
The total ion current .profile (TI'CP) is defined as a
normalized plot of the sum of the ion abundance
measurements in each member of a series of mass
spectra as a function of the serially indexed spectrum
number. Data for this plot are acquired by continuous,
repetitive acquisition of mass spectra as sample
components emerge from a gas chromatograph, leak
from a batch inlet system, or volatilize from a direct
inlet system. Each point on the ordinate is the
normalized sum of all the ion abundance data in a
single mass spectrum; and, each point on the abscissa
represents the spectrum number or a corresponding
unit of time.
This same plot is referred to as a reconstructed gas
chromatogram (RGC) but this nomenclature is not
preferred as it does not accurately define a TICP. An
RGC could just as well be the output of a flame
ionization detector, as redrawn by a draftsman.
Cathode Ray Tube Terminal. A TICP may be output
on a cathode ray tube (CRT) in a few seconds'or on a
pen and ink plotter in several minutes. Sample dialogue
for the CRT output is as follows:
SELECT MODE: CRT
FILE NAME: SAMP1
DOUBLE DISPLAY?: N_
TOTAL ION CURRENT PROFILE?: Y_
EXTRACTED I C PROFILE?: N^
If the user responds Y_to the DOUBLE DISPLAY
prompt before the carriage return, a TICP and a mass
spectrum may be displayed together. Mass spectra
outputs are discussed later. A response of Y_ to the
EXTRACTED I C PROFILE?: prompt leads to
dialogue which is used to display an extracted ion
current profile (EICP). This option is described in a
subsequent section.
Unless a TICP consists of only a few spectra, e.g., 25,
it cannot be compressed on a small CRT and still
permit the viewer to accurately select spectrum
numbers for other operations. Therefore, commands
exist to replot a TICP with a better view of a smaller
area. These commands, which are entered from the
keyboard after display of the TICP, are as follows:
E_ further dialogue requests the extreme left hand
spectrum number
C_ entered repetitively after E for subsequent
plots of narrower ranges of spectrum numbers
beginning with the designated left hand value
56
-------
R_ restore last plot before expansion
G_ the complete TICP is replotted
F_ further dialogue requests filename for a
different TICP
CTRL/L returns to the system prompt. Several
other commands ore available from the CRT keyboard
during viewing of these plots. These produce EICP and
mass spectra plots and are discussed in subsequent
sections.
Plotter. The program for output of a TICP on the pen
& ink plotter is more flexible than the CRT program.
The output dialogue is as follows:
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: Y_
FILE NAME: SAMP1
EXPAND BY: press return
However, in this case the spectrum number
resolution is fixed and quite adequate for selecting
spectrum numbers for other operations. A response of a
number between 1-100 to the EXPAND BY prompt,
causes the total ion current data to be multiplied by the
expansion factor before plotting. This will cause some
peaks to be plotted with flat tops indicating the
numerical data exceeds the range of the plot axis.
Baseline as well as peak values are multiplied by the
expansion factor. In general factors greater than about
five are not very useful.
Long TICP plots from GC runs are best displayed
immediately on the pen and ink plotter. The time
requirement of several minutes is not that long, the
quality plot will be needed ultimately for the record,
and considerable time will be expended replotting for
better viewing with the CRT. On the other hand the
CRT is excellent for fast preview of TICP plots and the
rapid examination of data from a single or several
closely spaced peaks.
MASS SPECTRA HISTOGRAMS
Once a TICP is available, mass spectra are selected
from individual peaks and these are used to identify the
compounds causing the peaks. As with the TICP, mass
spectra may be displayed on the CRT or the plotter.
Since a TICP often consists of hundreds of mass
spectra, and since it is often necessary to plot several
mass spectra per peak, the fast CRT is of enormous
value in previewing mass spectra. Ultimately, selected
spectra may be plotted on the pen and ink plotter to
make quality copy for reproduction in reports or for
preservation in the permanent record.
Cathode Ray Tube Terminal. The dialogue for CRT
output of mass spectra is as follows:
SELECT MODE: CRT
FILE NAME: SAMPLE
DOUBLE DISPLAY?: N_
TOTAL ION CURRENT PROFILE?: N_
SPECTRUM NUMBER: 3_
SUBTRACT BACKGROUND?: Y_
SPECTRUM NUMBER: 2_
In the CRT mass spectrum plot dialogue, a negative
response to a TICP causes the program to assume that
a mass spectrum is to be plotted. Normally the best
spectrum number is found on the leading edge of a
peak, about two-thirds of the way to the peak top. For a
single component peak, the spectra will not differ much
across the peak except for abundances at the very high
and low amu values. For a multicomponent peak,
several spectra can be used to determine which ions in a
spectrum belong to a single component. Background
subtraction is extremely important to remove
extraneous ion abundance data from the spectrum of a
compound. In addition to unresolved components,
these extraneous ions are generated from continuous
column bleed and background materials in the
spectrometer that are not pumped out rapidly.
Spectrum selection and background subtraction is
often an iterative process, and several trials may be
required to produce the optimum spectrum.
An affirmative response to the CRT double display
prompt allows simultaneous display of two plots. The
following dialogue illustrates the use of this feature to
display a spectrum with background subtracted on the
upper plot and the background spectrum on the lower
plot.
SELECT MODE: CRT
FILE NAME: SAMPLE
DOUBLE DISPLAY?: Y_
UPPER GRAPH PARAMETERS:
TOTAL ION CURRENT PROFILE?: N_
SPECTRUM NUMBER: 3_
SUBTRACT BACKGROUND?: Y_
SPECTRUM NUMBER: 2_
LOWER GRAPH PARAMETERS:
SPECTRUM NUMBER: 2_
SUBTRACT BACKGROUND?: N
57
-------
The CRT commands E^ C R, G_, F,_ and CTRL/L
are also available after mass spectral plotting. In this
case E sets the extreme left hand amu value. Another
command, S,_may be entered after viewing a TICP or a
mass spectrum. It requests a spectrum number for
plotting as well as information for background
subtraction.
Plotter. The program for plotting a mass spectrum on
the pen and ink plotter is more flexible than the CRT
program and also permits one to print digital mass
spectral data on the console printer or CRT as well as
plot on the plotter. The output dialogue used to plot a
mass spectrum is:
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N^
EXTRACTED ION CURRENT PROFILE: N_
PLOT SPECTRUM? Y_
FILE NAME: REF2
SPECTRUM NUMBER: 49
AMPLITUDE EXPANSION?: press return
MINIMUM VALUE %: J_
SUBTRACT BACKGROUND?: Y_
SPECTRUM NUMBER: 44
BACKGROUND AMPLIFICATION:
press return
SAVE SUBTRACTED FILE?: N_
NORMALIZE ON: press return
A plot of the reference compound mass spectrum using
the dialogue is shown in Figure 4.1. To illustrate
several of the plot options the following dialogue was
used to generate the spectrum in Figure 4.2.
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N_
EXTRACTED ION CURRENT PROFILE: N_
PLOT SPECTRUM?: Y_
FILE NAME: REF2
SPECTRUM NUMBER: 49
AMPLITUDE EXPANSION?: Y_
THRESHOLD %: 5_
EXPAND BY: 5_
MINIMUM VALUE %: 2_
SUBTRACT BACKGROUND?: Y_
SPECTRUM NUMBER: 44
BACKGROUND AMPLIFICATION: W
SAVE SUBTRACTED FILE? Y_
FILE NAME: REF2BS
NORMALIZE ON: press return
TITLE: DFTPP 5 1 75
SPECTRUM NUMBER: 49-44
BASE PEAK: 152320
TOTAL ION CURRENT: J_223424
An affirmative response to the AMPLITUDE
EXPANSION? prompt leads to dialogue in which a
per cent relative abundance threshold and an expansion
factor are entered by the user. The product of the
threshold and expansion factor may not exceed 30. The
principal application of this option is to emphasize very
weak ion abundances in the spectrum plot. The
minimum value option is used to eliminate plotting of
very weak abundances below the minimum. Normally
the minimum value and amplitude expansion options
are not used in the same plot. Background
amplification may be used to enhance the ion
abundance data in the background spectrum before it is
subtracted from the sample spectrum. If the user
chooses to save the background subtracted spectrum, a
file name must be supplied for the data. All spectra are
automatically plotted with the most abundant ion set to
100% relative abundance. However, a user may enter
an alternative mass number in response to the
NORMALIZE ON response, and the abundance of
that mass will be set to 100% with a proportionate
adjustment for all other abundances. This has the effect
of amplifying weak ion abundances without the scale
expansion shown in Figure 4.2
PRINTED MASS SPECTRAL DATA
Printed mass spectral data may be produced on
either the CRT or the console printer, but the OUTP
mode is required in both cases. Output is directed to
one or the other via the switch on the back of the CRT.
There are two possible responses to the PRINT
SPECTRUM?: prompt. A Y_response will cause mass
numbers, per cent relative abundances, and per cent of
total abundances to be printed. An A_ response will
cause mass numbers and the corresponding absolute
abundance data to be printed. Absolute abundances are
in analog-to-digital converter units. Standard printout
dialogue allows the user some of the same options as
the plotter routine:
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N_
EXTRACTED ION CURRENT PROFILE?: N_
PLOT SPECTRUM?: N_
PRINT SPECTRUM?: Y_
FILE NAME: SAMP2
SPECTRUM NUMBER: 42
58
-------
8
e.
8-
P-
bS.
8.
o
SPEOfUl
DFIPP S
V
30 10
nx e
rueat t
) IS
j j, ,
X SO
9 -
A
TO
tl
/!
eo SB 100
10 120
I ..!'.
tag IIB isa 10 no tao iao
,| 11(1 (
2nO Z10 ZE» 238 MO ZSB
. 1 , ' . .
a» ^ 280 SO » 310 320 3M 310 36D 3SO 370 380 330 «10 '«0 CO GO t
IB «0 1
Figure 4.1 The mass spectrum of a GC/MS reference compound, decafluorotriphenylphosphine.
-------
9>EEmjM Nraoi
HTTP s i TS
R.
r
WB-
» SB" i
IBB in ae
B SB V
iee us' ISB tag i« tan iw ITS
«a
za MS ZSB as ro a» ao sss sie fc 333 sra 3SB sso rw jaa 333 -as «a' «B 'CT «> iso
Figure 4.2 The mass spectrum of a GC/MS reference compound, decafluorotriphenylphosphine, with
plot options.
-------
PARTITIONED OUTPUT?: N_
MINIMUM VALUE %: 5_
SUBTRACT BACKGROUND?: Y_
SPECTRUM NUMBER: 40
BACKGROUND AMPLIFICATION:
press return
SAVE SUBTRACTED FILE?: N^
NORMALIZE ON: press return
TITLE: SAMPLE 2 2UL of 1ML
SPECTRUM NUMBER: 42 - 40
BASE PEAK: 327680
TOTAL ION CURRENT: 681283
PERCENT OF
AMU INTENSITY TOTAL INTENSITY
51.0
63.0
64.0
102.0
102.0
126.0
127.0
128.0
129.0
9.27
7.44
8.12
9.21
9.21
7.39
13.90
100.00
11.45
4.45
3.58
3.90
4.43
4.43
3.55
6.68
48.09
5.51
However, in place of the plotter AMPLITUDE
EXPANSION? prompt, the PARTITIONED
OUTPUT? prompt is printed. A Y_ response permits
the output of selected ion abundance data. The
following application of partitioned output shows data
from a spectrum of perfluorotri-n-butyl amine
(PFTBA). This spectrum was measured immediately
after calibration while PFTBA was in the spectrometer.
The partitioned output gives a rough idea of the
condition of the spectrometer.
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N_
EXTRACTED ION CURRENT PROFILE?:
PLOT SPECTRUM?: N_
PRINT SPECTRUM?: Y_
FILE NAME: J_
SPECTRUM NUMBER: j_
PARTITIONED OUTPUT?: Y_
MASS RANGE: 67-72; 219-222;
500-505; 612-616
N
: TITLE: PFTBA
SPECTRUM NUMBER: 1
BASE PEAK: .7215104
TOTAL ION CURRENT: 15664128
PERCENT OF
AMU
, 67.0
68.0
69.0
70.0
71.0
72.0
219.0
220.0
221.0
500.0
501.0
502.0
503.0
613.0
614.0
615.0
616.0
INTENSITY
.04
.49
100.00
1.38
-02
.00
25.23
1.09
.02
.00
.00
.84
.09
.00
.15
.02
.00
TOTAL INTENSITY
.02
.22
46.06
.63
.00
.00
11.62
.50
.00
.00
.00
.38
.04
.00
.07
.00
.00
MINIMUM VALUE %: press return
SUBTRACT BACKGROUND?: N_
NORMALIZE ON: press return
Partioned output of digital data is analogous to the
extracted ion current profile that is discussed in the
next section.
THE EXTRACTED ION CURRENT
PROFILE
The extracted ion current profile (EICP) is defined as
a plot of the change in relative abundance of one or
several ions as a function of the serially indexed
spectrum number. It is called an extracted ion current
profile because the data are literally extracted from the
total ion current profile (TICP) data in a non-real time
process. The EICP is therefore analogous to
partitioned output of digital data. However, it should
not be confused with real-time selected ion monitoring
(SIM) and the corresponding selected ion current
profile (SICP) that are discussed in Chapter 6. The SIM
technique is a real time process in which ion abundance
data are measured at only selected masses as
components emerge from the gas chromatograph or
other inlet systems. The SIM technique produces a real
increase in signal/noise by time averaging random
noise. The EICP produces an apparent increase in
sensitiyjty by removing from the TICP the ion
abundance data from background, unresolved
components, and other irrelevant ions. The terms
limited mass output or limited mass search are often
61
-------
used, but are less meaningful than extracted ion current
profile to describe this plot.
On the CRT, the EICP is generated by an affirmative
response to the TOTAL ION CURRENT PROFILE?:
prompt and an affirmative response to the
EXTRACTED I C PROFILE?: prompt. The user is
then requested to enter a mass or mass range. The CRT
commands E, C, R, G, and F are available as described
above, and an L command may be used to change the
mass range in the EICP plot. The dialogue for a CRT
EICP is as follows.
SELECT MODE: CRT
FILE NAME: SAMPLE
DOUBLE DISPLAY?: N_
TOTAL ION CURRENT PROFILE?:
EXTRACTED I C PROFILE?: Y_
MASS RANGE: 149
Y
In response to the MASS RANGE? prompt, the user
may insert up to eight individual masses or mass ranges
separated by semicolons. The EICP produced is a sum
of the abundance data for each of the masses or mass
ranges specified. Figure 4.3 shows a TICP and the
EICP for mass 149 from the same data file. The
compounds that produce mass 149 ions are clearly
highlighted in the EICP. The plotter output dialogue is
similar to the CRT dialogue.
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N^
EXTRACTED ION CURRENT PROFILE?: Y_
FILE NAME: SAMP1
MASS RANGE: 149
EXPAND BY: press return
QUEUED OUTPUT
The user may defer actual output of various pen and
ink plots and printouts until a series of output
commands have been stored for later execution. In
response to the system prompt, the user enters the
command QUEUE. The system immediately returns to
the system prompt. The user enters the information
required to generate an output. However, at the
completion of the dialogue the plot is not executed, but
the system returns to the system prompt. A series of
output dialogues may be completed by a repitition of
this procedure. The queue is ended with the command
ENDQ in response to the system prompt. All
commands are then sequentially executed. The user
must delete the $$ QUE file before another queued
output can begin. The following dialogue is an example
of a queue for two spectrum plots.
SELECT MODE: QUEUE
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N_
EXTRACTED ION CURRENT PROFILE: N_
PLOT SPECTRUM?: Y_
FILE NAME: 805D
SPECTRUM NUMBER: 34
AMPLITUDE EXPANSION?: press return
MINIMUM VALUE %: j_
SUBTRACT BACKGROUND?: Y_
SPECTRUM NUMBER: 3^
BACKGROUND AMPLIFICATION:
press return
SAVE SUBTRACTED FILE?: N_
NORMALIZE ON: press return
SELECT MODE: OUTP
TOTAL ION CURRENT PROFILE: N^
EXTRACTED ION CURRENT PROFILE: N_
FILE NAME: 81-6D
SPECTRUM NUMBER: 67
AMPLITUDE EXPANSION?: press return
MINIMUM VALUE %: \_
SUBTRACT BACKGROUND?: Y_
SPECTRUM NUMBER: 60
BACKGROUND AMPLIFICATION:
press return
SAVE SUBTRACTED FILE?: N^
NORMALIZE ON: .press return
SELECT MODE: ENDQ
4.2 THE MSSOUT OUTPUT SOFTWARE
This output system has many of the same 'basic
capabilities as the output and CRT software described
in section 4.1. However, the MSSOUT software has
flexibility and capabilities not found in the standard
output programs. This progam requires the presence of
an extended arithmetic element (EAE) in the PDP-8
computer. The EAE unit consists of two printed circuit
boards labeled M8340 and M8341. These provide
enhanced processing speed for certain types of
computer instructions.
The MSSOUT software also requires the presence of
seven files on the system disk: MSSOUT, MOUTP1,
MOUTP2, MOUTP4, MOUTP5, MOUTP6, and
INCCHR. Another file, SS1S, is generated by the
program. As with many other choices, there are
advantages and disadvantages to adopting the
62
-------
i oo no i:e 130 i« IEO ieo no too iso zoo 310 220 zio zte zso
EICP-MASS 149
zre ZBB zse SOB aio 320
aw jse JIB aro JBO iaj «B
Figure 4.3 The extracted ion current profile for mass 149 and the corresponding total ion current profile.
-------
MSSOUT software. The principal disadvantage, in
addi.tion to the hardware capital investment, is that a
set of user commands need to be mastered in order to
use the capability. The MSSOUT program is non-
prompting (non-interactive). The user must know what
commands to enter and their proper sequence. Another
disadvantage is that there is a bug in the MOUTP4 file
that has proven difficult to locate and repair. This bug
causes flat topped peaks that are really not saturated.
Another version of MOUTP4 exists in which the flat
topped peak bug was repaired, but spectra are
sometimes missed. A temporary fix is to retain both
versions on the system disk under other names. This
allows the user to delete the current MOUTP4 and
rename with the COPY program one of the versions.
The choice depends on which bug the user wants to live
with. The file MTP4/1 is a version of MOUTP4 that
gives flat topped peaks; the file MTP4/2 gives missing
spectra.
The advantages of the program appear to be very
significant and include the following:
1. The user has the capability to designate within
limits the size of various plotter displays and
alphanumeric labels.
2. The user has the ability to switch rapidly
between CRT and plotter displays within the
same program.
3. Because of the EAE hardware, processing
speed is improved somewhat compared to the
standard software.
4. Mass spectra histograms may be plotted over a
smaller mass range than was actually observed
during the original .data acquisition. Therefore
if the 33-450 amu range was observed, but no
ions were observed above mass 300, the
histogram plot may be limited to 33-300 amu.
5. Similiar capabilities exist for Total Ion Current
Profile (TICP) and Extracted Ion Current
Profile (EICP) plots, i.e., portions of
chromatograms that contain the peaks may be
plotted, and the leading or trailing sections
that contain no peaks may be deleted from the
graphics display.
The MSSOUT outputs all begin with the same basic
dialogue:
SELECT MODE: MSSOUT
RUN NAME: STD
NBS STD SONG EACH
In this dialogue the run name means the same as the
filename in the standard output software. After the run
name is entered, the program immediately prints the
title attached to that file. If an informative title was
entered, this will confirm the identity of the data file.
After this an asterisk is printed. This is a signal that the
program is ready to receive commands from the user. If
the user wishes to change the data file (run name) this
may be accomplished anytime after an asterisk is
printed. Simply enter the NA (name) command and the
program returns to the RUN NAME: prompt.
NA
RUN
NBS
NAME: 213
SAMPLE 213 5UL
Anytime after an asterisk is printed the user may
enter the EX (exit) command which causes the
program to return to the system prompt. The user
commands for various outputs are described in the
following sections. These are organized similarly to
section 4.1 with sections on the TICP, Mass Spectra
Histograms, and Printed Mass Spectral Data, the
EICP, and Queued Output.
THETOTAL ION CURRENT PROFILE
The sequence of commands in the sample dialogue
will cause a TICP to be plotted on the plotter. The
TICP will begin at spectrum number 20 and end at
spectrum number 220. The plot will be 3 inches high by
5 inches long. Figure 4.4 is the result of these
commands:
*CM
ENTER MASSES TO COLLECT.
MAX= 24
*EM
ENTER MASSES TO PLOT
J_
ST=20
*EN = 220
HE = 3
LE =
.pp
SCAN
64
-------
TJJ
50 100 150 200
Figure 4.4 A total ion current profile generated with MSSOUT
-------
s
STD
lOO-i
80-
60-
40-
20-
SCAN 216
i
r25
Vf*
) "I-f r | » ; v yr( i [ » |"» ; » (
50 100 150 200 250 300
Figure 4.5 A mass spectrum plot generated with MSSOUT
-------
This sample dialogue illustrates the use of some of
the commands that may be used to generate a TICP.
The CM (collect masses) command is mandatory and
causes the program to gather and save in core memory
the data necessary to plot a TICP and, optionally, a
number of EICP's. If the user responds with a
RETURN to the ENTER MASSES TO COLLECT
prompt, as was done in the example, only data for a
TICP will be collected, and it will not be possible to
display an EICP. However the user may reenter the
CM anytime an asterisk is printed, and cause the
program to collect a new set of data. The MAX=X
gives the maximum number of EICP's that may be
saved in core memory, and this is explained further in
the section on the EICP. If MAX=0, the data for a
TICP is saved after entering RETURN. If specific
masses are entered, the data necessary for a TICP is
always gathered in addition to the EICP data.
The EM command is optional in the most recent
version of MSSOUT, and this revision should be placed
on all disks. The functions of the EM command are
explained in the section on the EICP.
The ST (start) = X (where X = an integer spectrum
number) and EN (end) = X commands are optional,
and allow the user to define starting and ending
spectrum numbers for the TICP. If these commands
are omitted, the default values are the first and last
spectrum numbers in the file.
The HE (height) = X (where X= integer inches)
and LE (length) = X commands are also optional, and
apply to the plotter only, not the CRT. They allow the
user to define the height and length of the plot up to the
maximum size of the paper. If these commands are
omitted, the default size is 5x8 inches. The final
command that must be entered is either a PP for a plot .
on the plotter or a PM for a display on the CRT.
An extremely important feature of MSSOUT is that
the values entered for all commands are saved until
they are changed or until the program is restarted. This
feature results in a number of convenient possibilities
for the user. For example one may issue a PP
immediately after a PM and produce the same plots on
the- plotter and CRT. Alternatively, the user may
change just one or two commands then enter the PP or
PM, and immediately produce a modified plot without
reentering all the commands. The command OP
(options) will print out a list of all current command
options, and this should be used in the event the user
needs to recall the current option selections. The values
of the options shown in the following list specify the
default values, and these will be used for all plots until
they are changed by the user. In some cases, e.g., HE,
the actual default value is given; however in most cases,
e.g., CM, a zero specifies the default situation.
*OP
CO
ST
EN
BA
MA
LI
HE
LE
TH
CS
LA
FR
CM
SM
MC
su
SF
0
0
0
0
0
0
5
8
1
0
50
Y
0
0
S
0
100
These option values are saved during a terminal session
even though the user changes the data file with the NA
command.
An IN (integrate) command also exists to integrate
peak areas. However, this is discussed in section 6.2
along with other quantitative analysis methods. If the
data was acquired with the RIB interface and time data
was stored with the datafile, MSSOUT may be used to
give plots with time in minutes on the x axis. Setting the
parameter MC=T gives the time axis. The default
value is MC=S or spectrum number.
MASS SPECTRA HISTOGRAMS
The sequence of commands in the sample dialogue
will cause a mass spectrum to be plotted on the plotter.
A background spectrum will be subtracted, and the
plot will begin at mass 50 and end at mass 310. The
filename (run name), spectrum number (scan number),
and axis labels will be in one-quarter inch high
characters. The size of the plot will be 6 x 8 inches.
Figure 4.5 is the result of these commands:
*SC
SCAN
216
*SU
ENTER
NUMBERS:
BACKGROUND: 213
67
-------
300-
80-
60-
40-
20-
STD SCAN 236
*t»,HJrr^
r25
X30
50 100 350 20O 25O 3OO
Figure 4.6 A mass spectrum plot generated with MSSOUT
-------
'ST=50
EN = 310
CS =
*LE =
*PL
The SC command is mandatory for a mass spectrum
plot and the spectrum number is requested. Several
spectra may be specified by a series of spectrum
numbers separated by commas. The only other
mandatory command is either a PL for a plot on the
plotter or a DI for a display on the CRT. After a
spectrum is displayed on the CRT, entry of a return
will cause the CRT to be paged for the next spectrum, if
more than one was specified, or the next command. If
more than one spectrum is specified with the SC
command, and output is to the plotter, the plots are
queued automatically one after the other. There are a
large number of optional commands that may be used
to refine these graphics outputs. Some of these apply
only to displays on the CRT, some apply only to plots
on the plotter, and some apply .to both outputs.
All of the following options apply to both the CRT
and plotter. The SU command causes a background
subtract prompt. If more than one background
spectrum is specified, the background subtraction
process appears to be aborted, but no error message is
output by the program. The ST (start) = X (where X
= an integer mass) command defines the starting mass
of the plot, and the EN (end) = X command defines
the ending mass of the plot. The default values for ST
and EN are the first and last masses observed. The BA
= X (where X = an integer mass) may be used to
specify the mass used to normalize the mass spectrum
plot. The default value is the base peak in the spectrum.
The LA = X (where X =.an integer mass) may be used
to specify the mass interval between labeled tick marks
on the mass axis of a spectrum plot. The default value is
50 amu. The SF = X (where X is a integer factor) may
be used to specify the amount of amplification of the
background spectrum before background subtraction.
The default value is 100 which corresponds to an
amplification factor of one. Therefore entry of SF =
150 will amplify the background file by 50%. Entry of
SF = 50 will reduce the background spectrum by a
factor of two. The MA = X, Y (where X = an integer
mass number and Y = a magnification factor) may be
used to specify that beginning at mass X all ion
abundances are to be multiplied by the factor Y before
plotting. The mass where magnification begins is
indicated on the plot as in Figure 4.6. The capability to
average several spectra, e.g., across a TICP peak, is
another optional procedure which is accomplished
with the dialogue:
SC
SCAN NUMBERS:
A_
AV
ENTER SCANS TO AVERAGE: 214-220
The average spectrum plot is completed with the other
standard commands as above.
A summary of optional commands that apply to the
plotter and the CRT is as follows:
SU Subtract background
ST Starting mass
EN Ending mass
BA Normalize on
LA Interval of mass axis labels
SF Background amplification factor
MA Ion abundance multiplier
A/AV Average spectra
As previously described under the total ion current
profile, values entered for most of these options are
saved until changed or until the program is restarted.
The current values or default values of the optional
commands may be printed with the OP command. A
command RE (repeat) is also available for mass
spectrum plots. This causes a repeat of the plot that was
most recently requested.
There are three commands that apply just to CRT
displays. The DI command is the command which
causes the actual CRT display and this was described
above. The LI = X (where X = a low integer value,
e.g., 1,2, or 3) is an option that defines the number of
horizontal regions the CRT is divided into for an
expanded presentation of -a mass spectrum. The
. practical limitation of LI is probably 3 or 4, and the
default value is selected by the program depending on
69
-------
the mass range scanned. Finally the CO = X (where X
is an integer) command may be used to automatically
make X number of hard copies of the CRT display.
There are several commands that apply just to the
plotter. The PL command causes the plot to begin, and
this was described above. The FR command causes a
line (frame) to be drawn across the top of the mass
spectral plot. The DF comand deletes this frame and is
the default choice. The HE = X (where X = height in
inches) and LE = X commands have the same
meaning as described under the total ion current
profile. These options may be used to specify the size of
the plot within the limits of the paper size. The default
size is 5 x 8 inches. Finally the CS = X (where X = an
integer value) may be used to define the size of the
alphanumeric characters used in the plot labels. A size
of one inch is expressed by CS = 100, one half inch by
CS = 50, and one-quarter inch by CS = 25, etc.
In summary, the commands that apply either to the
CRT or the plotter, but not both are as follows:
DI Begin CRT plot
LI Division of CRT into regions
CO Automatic CRT copies
PL Begin plotter plot
FR Draw line on top of histogram
DF Delete line
HE Set height of plot
LE Set length of plot
CS Define character size
PRINTED MASS SPECTRAL DATA
Lists of digital data may be printed on the CRT or
printer using the commands TA and RD. The TA
command gives a normalized list and the RD
command generates raw data in terms of analog to
digital converter counts. A spectrum number or
numbers must be specified first with the SC command.
THE EXTRACTED ION CURRENT
PROFILE
The EICP plot is a variation on the total ion current
plot, and all the commands that apply to the TICP also
apply to the EICP. However the method of using the
CM and EM commands is crucially important. The
CM (collect masses) command is required as in the
TICP, but the individual masses of interest must be
specified in response to this command. Mass ranges are
not accepted as a response to the CM command. The
printed message that follows the CM command
informs the user of the maximum number of individual
masses that may be specified. This maximum will vary
as a function of the size of the data file.
'CM
ENTER MASSES COLLECT.
143,167,193,208
MAX= 24
After the collection is completed the user may
display the plots in a number of sequences, and create
other types of plots. These very flexible options are
described in this section. The most basic option is to
display the EICP's specified in exactly the order and
quantity given in the CM command. This may be
accomplished on the CRT or plotter, but the TICP is
always placed on the bottom of the display. The EICP's
are then placed in order, from the bottom to the top, as
they were listed with the CM command. This list is
saved until another CM command is issued, or the
program is restarted.
The functions of the EM command are to redefine
the order in which various plots are displayed on a
single CRT or plotter display, and to generate subsets
of the plots specified in the CM command. For
example, if the EM command below were entered, the
sequence of plots" from the bottom to the top of the
display would be a TICP, a mass 169 EICP, a sum plot
(defined later), a TICP, a mass 197 EICP, a mass 213
EICP, and another TICP.
*EM
ENTER MASSES TO PLOT
T,169,S,T,197,213,T
Figure 4.7 is an example of this type of display using a
different response to the EM command. The sequence
of plots defined in the EM command is saved until
another EM command is issued or the program is
restarted, but the current value of EM does not appear
in the options list. Mass ranges are not accepted by the
EM command.
The EM command may also be used to define subsets
of masses prior to the IN (integrate) command that is
described in section 6.2.
The sum plot referenced above displays the sum of
the abundances of two or more masses. The S response
to EM is not functional until a sum is defined by the SM
command as follows.
"CM
ENTER MASSES TO COLLECT. MAX =
143,167,193,200
24
70
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Ld
f- <
C/O CQ
250
Figure 4.7 An extracted ion current profile generated with MSSOUT
-------
EM
ENTER MASSES TO PLOT
S_
*SM
ENTER M/E'S TO SUM
143, 167,193
*PP
SCAN
This dialogue produces a single plot that is an EICP for
the sum of the abundances of the three masses
specified. There is one other command, the BA = X
(where X is an integer mass), that may be used to
specify the. abundance used to normalize any EICP
plot.
In summary the commands that may be used for the
EICP are as follows:
PP Causes actual plot on the plotter
PM Causes actual plot on the CRT
ST Defines starting spectrum number
EN Defines ending spectrum number
HE Defines height of plot on the plotter
LE Defines length of the plot on the plotter
SM Requests abundances to be summed
BA Normalize EICP on mass
The user should note that Figure 4.7 has a line drawn
across the top of each EICP and that this may not be
deleted with the DF command because this command
does not apply to TICP and EICPs.
QUEUED OUTPUT
Queued output of a series of separate displays with
MSSOUT is only possible with mass spectra plots. The
user should enter, in response to the message printed
after the SC command, a series of spectrum numbers
separated by commas. The SU command may be used
to subtract the same background spectrum from each.
After each spectrum is plotted on the CRT, pressing
the return causes the program to immediately produce
the next plot. However if a CO command is used, an
automatic hard copy of each will be generated, and the
next spectrum produced without the return. A similar
series of plots may be queued to the plotter.
4.3 INTERACTIVE GRAPHICS
ORIENTED OUTPUT
SOFTWARE (IGOOS)
This output system has many of the same Basic
capabilities as the plotter and CRT software described
in sections 4.1 and 4.2. However, the IGOOS has
significant additional capabilities not available with the
previously described output systems. This software
requires the presence of an extended arithmetic element
(EAE) in the PDP-8 computer. The EAE unit consists
of two printed circuit boards labeled M8340 and
M8341. These provide enhanced processing speed for
certain types of computer instructions.
The standard TICP and EICP capabilities require
the presence of three files on the system disk:
BCLRGC, RGCOV1, and RGCOV2. Mass spectrum
plotting requires the files CRTPLT, PLOVL1, and
PLOVL2. As with many other choices, there are
advantages and disadvantages to adopting the IGOOS.
The principal disadvantage, in addition to the
hardware capital investment, is that a set of user
commands need to be mastered in.order to use the
capability. The IGOOS has its own set of commands
and the user must know what commands to enter and
their proper sequence. Another disadvantage is the
presence of several program bugs. These are
documented along with the user instructions. The
advantages of the program appear to be very significant
and include the following:
1. The user has the capability of selecting
spectrum numbers from CRT graphics
displays by placing the cross hair cursors over
the appropriate place on the display, and
entering a single character command at the
keyboard.
2. The convenient spectrum number selecting
capability described above may be used to
build Q files consisting of spectrum numbers
and corresponding background spectrum
numbers. These Q files may be used to drive
other programs that plot spectra on the CRT
or plotter, that abbreviate spectra for matching
against a local or remote database with a
spectrum matching program, or that perform
quantitative analyses.
3. The same basic software may be used to
generate CRT and plotter displays of various
graphics, with the CRT used as a convenient
preview of what will appear on the plotter.
72
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4. Because of the EAE hardware, processing
speed is improved somewhat compared to the
software described in section 4.1.
5. Finally there is the capability to display TICP
and EICP plots exactly above one another on
the CRT or plotter. Up to six plots can be
overlayed in this way.
TOTAL AND EXTRACTED ION
CURRENT PROFILES
The user entry into this program is with the
following dialogue which specifies the first TICP or
EICP to be displayed on the CRT:
SELECT MODE: BCLRGC
FILE? CINTAP
Q-FILE NAME?
RANGE?
EXPAND BY?
QCINTA
In response to the FILE? prompt the user enters the
'data filename. A Q-filename must be entered even
though the user has no intention of setting up a Q file.
The program will perform if a RETURN is entered in
response to the Q-FILE NAME? prompt, but an
unnamed Q file will result if a Q file is initialized, and
this will cause problems. If a Q file is not initialized and
closed as explained below, the Q-filename will not be
saved in the disk directory. In response to the
RANGE? prompt the user may enter a RETURN for a
TICP or a single mass or mass range for an ELCP. In
response to the EXPAND BY? prompt the user enters
a RETURN for no expansion, or an integer number
which is a multiplication factor for profiles containing
only weak peaks. A CRTL/L during this or any
subsequent dialogue causes a return to the system
prompt.
At this point the designated TICP or EICP is
displayed on the CRT screen, and the cross hair cursors
are activated. If the data file consists of 260 or fewer
mass spectra, the entire TICP or EICP will be
displayed. If the file contains more than 260 spectra,
only the first 260 points are displayed. A block of 260
spectra is referred to as a screen load. The TICP's and
EICP's are displayed in 260 spectra screen loads in
order to allow sufficient accuracy in positioning of the
cross hair cursor on a given spectrum number.
With the first screen load displayed the user has only
two options. Entry of a series of RETURNS will cause
all sections of the TICP or EICP id be displayed in
screen loads of 260 spectra with a 20 spectra overlap
between each. Alternatively with any given screen load
the user may initialize a Q-file by entry of the character
Q. This will activate the S and B keys until Q is entered
again which closes the Q-file.
With the S and B keys activated the user may save
spectrum numbers in the Q-file by positioning the
horizontal and vertical cross hairs over the desired
point on the profile, and striking S or B. The S key is
normally used to save spectrum numbers
corresponding to the apexes of peaks, and the B key is
used to save the corresponding background spectra.
The B key cannot be used except after an S is entered.
However, a succession of S's may be entered without
saving any background spectra. The spectrum numbers
saved are not required to correspond to apexes and
background. For example, they could be used to save
spectrum numbers that correspond to the limits of
intergration for a quantitative analysis program.
Entering a RETURN will cause the next screen load to
be displayed while the Q file is still open. At the
conclusion of the saving of all spectrum numbers, the Q
key must be pressed to close the Q file and cause it to be
saved in the disk directory.
After the last screen load of a given data file is
displayed, certain single character commands are
activated to permit other displays or plots. These
commands are the O, RETURN, F, R, and H. Several
of these commands return to the RANGE? prompt for
: specifications for displays, and several others cause the
program to remember or forget previous specifications
for CRT plots.
Entry of an O causes the program to return to the
RANGE? prompt for specifications for another TICP
or EICP that will be overlayed on the first plot on the
CRT. Up to six plots may be overlayed on the CRT,
and the program remembers which was specified first
and most recently. There is a reported bug in the O
option that may be present in other options. The bug
appears only when a Q file is initialized during the
viewing of a TICP. If the same TICP is overlaid with an
EICP using the O option, the TICP is displayed
incorrectly. x
Entry of a RETURN causes the program to forget
all specifications for previous displays and return to the
RANGE? prompt.
Entry of an F causes the program to forget all
specifications for previous displays except the first, and
to display the first TICP or EICP specified on the CRT.
This command has a slight bug in some versions of the
program. It assumes the first display specified was a
TICP; but, if it was an EICP,- the data will be displayed
correctly, but the EICP will be labeled a full mass range
plot.
73
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Entry of an R causes the program to forget all
specifications for previous displays except the first, and
to return to the RANGE? prompt for specifications for
a TICP or EICP. This is then displayed on the CRT
overlayed with the first plot specified.
Entry of an H causes the last TICP or EICP specified
to be plotted on the plotter. Before this begins the
OVERLAY? prompt is printed. A negative response
causes the plotter to draw the spectrum number axis
first. An entry of Y_ causes the plot without the axis.
The program then returns to the COMMAND?
prompt. At this point only the O and R as defined
above have any meaning. A RETURN causes the
program to return to the RANGE? prompt and forget
about all previous specifications.
MASS SPECTRA HISTOGRAMS
For mass spectra displayed on a CRT or plotter the
dialogue is as follows:
SELECT MODE:
FILE? CINTAP
SPECTRUM?
CRTPLT
A summary of all commands is as follows:
Character Function
Q Initialize or close a Q
file of spectrum numbers
S Save a spectrum number
designated by the cross
hair cursors in a Q file
B Save a spectrum number
designated by the cross
hair cursors in a Q file ;
RETURN Display next screen load
on a CRT
O Overlay the next TICP or
EICP specified on the CRT
RETURN Forget all information
about previously specified
TICP's or EICP's and return
. to the RANGE? prompt
F Forget all information
about specified TICP's or
EICP's except the first,
and display it on the CRT
R Forget all information about
previously specified TICP's
or EICP's except the first,
and overlay it with the next
one specified on the CRT
H Plot the last specified
TICP or EICP on the plotter
When Operable
Anytime
After a Q file
is initialized
After an S command
Before final screen
is displayed
After final screen
is displayed
After final screen
load is displayed
After final screen
load is displayed
After final screen
load is displayed
After final screen
load is displayed
74
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The response to the FILE? prompt is the usual data
filename. There are three possible responses to the
SPECTRUM? prompt. Entry of a spectrum number
leads to the additional prompts as follows:
SPECTRUM? 2_
BACKGROUND SPECTRUM? ]_
AMPLIFY BY?
If no background subtraction is desired, the user should
press RETURN. Entry of a background spectrum
number leads to the AMPLIFY BY? prompt. An
amplification factor of 1-4 may be optionally entered.
This causes multiplication of the background spectrum
by the factor before it is subtracted. Generally this
feature is not useful, and the user should press
RETURN. At this point the spectrum is displayed on
the CRT, and the cross hair cursors are activated.
Interactive examination may begin as described later in
this section. To return to the SPECTRUM? prompt,
press RETURN.
In place of the entry of a single spectum number as
described above, the user may enter the commands QC
or QP. Both commands tell the program that the
spectrum numbers for the displays are to be retrieved
from a Q file generated by BCLRGC. The QC
command causes plots on the CRT, and the QP
command causes plots on the plotter. Each command
leads to the Q-FILE? prompt:
SELECT MODE: CRTPLT " '
FILE? CINTAP
SPECTRUM? QC
Q-FILE? QCINTA
It is extremely important that the user enter a true Q
filename generated by BCLRGC. Simply pressing
RETURN causes the program to hang, and there is no
apparent recovery procedure. Entry of a -non-existent
filename causes the program to generate spectrum plots
from apparently random numbers that have no
apparent meaning.
With the QP command a series of spectra denned by
the Q file are plotted on the plotter without further
operator action. The plotter program keeps a record of
the length of each plot. Therefore, if the pen is set
initially one inch to the right of a paper fold, each new
spectrum will be started one inch to the right of a fold.
When the Q file is exhausted, the program returns to
the system prompt.
With the QC command the first spectrum defined by
the Q-file is displayed on the CRT, and the cross hair
cursors are activated. Interactive examination of the
spectrum may begin, or the user may press the
RETURN to observe a CRT plot of the next spectrum
in the Q-file. When the Q-file is exhausted, the program
returns to the system prompt.
Regardless of how CRT plots are generated, i.e., by
entering individual spectrum numbers or with a Q-file,
interactive processing is possible when the cross hair
cursors are displayed. Four commands have special
meaning, namely B, E, R, and H.
The B command is used to blow-up (expand) a
section of a spectrum defined by the cross-hairs. To use
this command, first place the cross hairs over the
smaller of the two masses that define the section to be
expanded, and press B. Then place the cross hairs at the
larger mass and press B again. The section defined will
be expanded to the maximum extent possible. If the
larger mass is denned first, the program blows up.
The E command is used to multiply all abundances
by a single integer expansion factor. The masses to
which the expansion factor will apply are defined by the
position of the cross hairs. To use this command, place
the cross hairs over the mass that defines the starting
point for abundance expansion, e.g., mass 300, and
press E. This causes the EXPAND BY? prompt to be.
printed. Enter an integer expansion factor, e.g., 10,
press return, and the display will be redrawn with all
abundances above mass 300 multiplied by 10.
The R command restores the original spectrum to
the screen. The B and E commands are cumulative and
act on the current screen display, but R always restores
the original spectrum. The H command causes the
current CRT display to be plotted on the plotter. If this
is the last spectrum of a Q-file, the program returns to
the system prompt. Pressing a RETURN will either
cause a CRT display of the next spectrum in the Q-file,
or a return to the SPECTRUM? prompt if not in the Q
'mode. Any time a prompt is printed on the screen the
user may enter CTRL/L and return to the system
prompt.
EXTENDED MEMORY OUTPUT
SOFTWARE
The program SPRRGC performs very much like
BCLRGC except that it requires 16K of core memory,
and the TICP or EICP is generated using only the
abundances that maximize at each spectrum number.
For example, if the mass 149 abundances at spectrum
. nuinbers 100, 101, and 102 are 40, 90, and 40
respectively, the abundance at spectrum number 101
would be retained and the abundances at spectrum
75
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numbers 100 and 102 would be discarded. The program The program SPRPLT, and its overlay SPRVL1,
uses the overlays RGCOV1 and RGCOV2. A minor display spectra analogous to CRTPLT, but produce
difference from BCLRGC is that if the full mass range only mass maximized spectra as described above. One
measured is selected for display, the first mass scanned difference is that the RESOLUTION?: prompt, is given
is ignored. This was intended to compensate for some and the only legal responses are 1, 2, or 3. The exact
noise caused by some interfaces that gave false meaning of this resolution is not clear. There is no
abundance data at the first mass measured. The provision for background subtraction, but the QC and
program SPRRGC will not function correctly if QP commands are enabled as are the interactive
saturated peaks are present in the data file. options described under CRTPLT.
76
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CHAPTER 5
COMPOUND IDENTIFICATION
The compound identification chapter is not intended
to give complete, step-by-step instructions on how to
identify organic compounds by mass spectrometry.
That would be virtually impossible. The purpose of this
chapter is to set into perspective the techniques that are
available for compound identification. Major emphasis
is on quality assurance which is of utmost importance
in the environmental field, and guidelines for accurate
identifications are presented to assist the users of.
GC/MS systems.
5.1 INTERPRETATION FROM
THEORY
Interpretations of mass spectra for compound
identification may be attempted based on the theory of
mass spectra and the rules of fragmentation of organic
ions in the gas phase. Unfortunately, this approach is
frequently slow and tedious and generally requires
considerable experience. It is often difficult to sustain
the necessary accurate deductive reasoning process for
the long periods of time required to make a large
number of correct identifications. Finally, not enough
is known about the detailed processes that occur in the
fragmentations of organic ions, and this severely limits
the approach. However, when all else fails, this
approach is clearly justified in important situations,
such as an enforcement action or a fish kill.
This method will not be considered further in this
manual. However, a number of references to excellent
books are included in the bibliography, and many of
these discuss interpretation of mass spectra.
5.2 EMPIRICAL SPECTRUM
MATCHING
The purely empirical method of searching a file of
reference mass spectra to find a similar or exact match
of an experimental mass spectrum has been under
development for a number of years. Any empirical
search and match system has two fundamental
components: a data base, which is nothing more than
an organized collection of reference spectra, and a
system to search the database. Databases may be in
printed or machine readable forms and countless
search systems are possible. In this chapter several
printed spectral collections are recommended and
computerized spectral search systems are discussed.
SEARCHING PRINTED DATABASES
Manual searching of printed databases was
developed long before computerized systems, and some
elaborate indexing schemes were invented to facilitate
the user's search. Nevertheless, all manual search
systems are rather slow, subject to human error, and
intellectually fatiguing. It is also difficult and expensive
to update the database since the index usually requires
complete revision. In spite of these limitations, this
method may be rewarding for small numbers of
unknowns if a printed database is available.
For manual searches, the two most useful mass
spectral catalogs are the "Eight Peak Index of Mass
Spectra", published by the Mass Spectrometry Data
Centre (MSDC), Aldermaston, England, and the
"Compilation of Mass Spectral Data" (10 peak index)
by Cornu and Massot. (See the Bibliography for further
information.)
The "Eight Peak Index" consists of three tables in
three volumes (31, 101 spectra):
Volume 1.
Table 1. Spectra are arranged in ascending
molecular weight order, subordered on
number of carbon atoms, hydrogen atoms, etc.
Volume 2.
Table 2. Spectra are arranged in ascending
molecular weight order, subordered on m/e
values in order of decreasing abundance.
Volume 3.
Table 3. Spectra are arranged in ascending
77
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rn/e value order, each given where present as
first, second, and third most abundant;
subordered on other m/e values in order of
decreasing abundance.
An enlarged edition of the Compilation of Mass
Spectral Data (10 peak index) was published in 1975 in
two volumes with three sections. This edition contains
mass spectral information on 10,000 comounds.
Part I. Spectra are ordered by molecular weight,
giving the compound name, reference number
in the original collection, molecular weight,
molecular formula, and a listing of the 10 most
intense peaks and their abundances.
Part II. Spectra are ordered by molecular formula
(in order of C,H,D,Br,Cl,F,I,O,P,S,Si, and
others) and includes the same information as
Part I.
Part III. Spectra are ordered by frangment ion
values in order of increasing m/e values, and
includes the 10 most abundant peaks.
The "Eight Peak Index" is usually examined first,
because it contains three times as many spectra.as the
"Compilation of Mass Spectra". In both catalogs, the
fragment ion index is the most useful. Detailed
instructions for use of these catalogs is beyond the
scope of this manual, but these instructions are
included in the respective catalogs.
Perhaps the most difficult part of manual searching is
the judgment of how well a reference and experimental
spectrum match. Most spectra in the catalogs were
measured with magnetic deflection mass
spectrometers. There is a widespread belief that spectra
measured with quadrupole and other types of
spectrometers do not agree with spectra from magnetic
deflection spectrometers. However, this problem is not
at all serious when the spectrometer is tuned according
to procedures in chapter 2. With proper ion abundance
calibration, quadrupole measured spectra often agree
within a few percent with magnetically measured
spectra. Other factors, such as differences in inlet
systems, should cause greater spectral differences, but
these are difficult to recognize in spectral collections.
Comparisons of printed lists of masses and
abundances are especially tedious and it is
recommended that final decisions concerning matches
be made with the histogram plots in the "Registry of
Mass Spectral Data", Volumes I-IV, by Stenhagen, et.
al. There is also available the "EPA/NIH Mass
Spectral Data Base" published by the National Bureau
of Standard's Office of Standard Reference Data. This
presents the 25,566 spectra of the NIH-EPA collection
in bar graph form. The spectra are ordered by
molecular weight and each includes the molecular
formula, molecular structure, Chemical Abstracts
Service registry number, and compound name. The
publication is designated NSRDS-NBS 63 and the first
supplement will contain about 8000 additional
spectra.
REMOTE COMPUTERIZED
SEARCH SYSTEMS
The application of computers overcomes some of the
problems of manual searching, but computerized
search systems are constrained by the size and validity
of the database, the thoroughness of the searching
algorithms, and the cost of using the systems.
An excellent mass spectral search system (MSSS) is
available on a commercial time sharing system at a
moderate cost. This MSSS was developed with the joint
and cooperative support of the Mass Spectral Data
Centre - an agency of the British Government, the
National Institutes of Health, the U.S. Environmental
Protection Agency, and several other agencies. The
principal feature of the MSSS is that it provides
different search options and a single database in one
convenient system. Table 5.1 lists the many different
search options currently available.
Table 5.1. User Options Available with the Mass
Spectral Search System
Command Function
PEAK Finds all spectra that contain masses and
abundances that are designated by the
user '
MW Finds all spectra of compounds with a
molecular weight that is designated by the
user.
MF Finds all spectra of compounds with a
complete molecular formula that is
designated by the user.
KB Computer to computer transmission of
spectral data for matching; best for large
amounts of data; Biemann algorithm
PMW Combines peak and molecular weight
searches; powerful if you know the
molecular weight.
PMF Combines peak and molecular formula
searches; powerful if you know the
molecular formula.
78
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Command Function
MWMF Combines molecular weight and
molecular formula searches; fastest way
to find the spectrum of a known
compound.
SIM Computes a similarity index between two
sets of data; automatic on KB search.
SPEC Prints all masses and abundances from
spectra in the file; user must supply an
identification number.
FICHE In manual mode, prints fiche numbers
and matrix positions of spectra in the file;
user must supply an identification
number; also in computer mode may
drive one model automatic fiche viewer.
PLOT Plots mass spectra from the file on a
graphics device; user must supply an
identification number.
COM User may enter comments, complaints,
and suggestions.
NEWS Prints news of the system
EXIT,
END,OUT Causes the mass spectral search system
to fade away.
AUTH Searches for literature references by
, specific author.
COMP Searches for literature references by
specific compound.
ELE Searches for liteature references by
specific elements.
HELPxxxx Prints explanation of the option xxxx.
INDEX Searches literature references by specific
index terms.
LAB Calculates the enrichment of isotopically
labeled compounds.
META Calculates the m/e values of various
metastable ions that correspond to a given
parent/daughter pair.
MOLFOR Calculates all possible molecular
compositions that have approximately the
same accurate mass.
PBM A reverse mass spectral matching
program..
PF Finds all spectra of compounds with a
partial molecular formula that is
designated by the user.
PA Searches for proton affinities
SUBJECT Searches for literature references by
specific subject.
OPT.HELP Prints this list of options
For all of the spectral search options in Table 5.1
except KB and PBM, the user enters mass, abundance,
or other data from a keyboard/printer or
. keyboard/cathode ray tube (CRT) terminal that is
interfaced to a conventional voice grade telephone line.
This terminal may be completely independent of any
GC/MS data system. Data entered by the user are
transmitted to the time sharing computer that searches
the database and prints interim search results at the
user's terminal in a few seconds. The user employs
these interim results to make judgments about
additional data to be entered to improve the search
results. This interactive, iterative procedure may
continue until the user is satisfied that the database was
thoroughly searched. The usual result is that a small
number of spectra are found and reported by
identification numbers and names. The final choice
.among these is the responsibility of the user. Complete
spectra may be printed at the user's terminal or plotted
on a graphics device.
With the KB option, a completely different mode of
operation is employed. This is not an interactive,
iterative option, but a number crunching system to find
the best overall match using the Biemann search
algorithm. Most importantly, with the KB option data
may be transmitted automatically from the mini-
computer of the GC/MS data system to the time
sharing computer or entered from a keyboard. The
remote computer conducts a search for a match based
on the transmitted mass and abundance data, and sends
the results back to the mini-computer in a matter of
seconds. Direct, computer controlled data transfer
requires special communications hardware and several
programs for the GC/MS data system. The hardware
and programs are available for a number of mini-
computers commonly used in GC/MS data systems.
The choice between automatic transmission or one of
the keyboard entry options depends on the
circumstances. For a few spectra or for special feature
searches, e.g., by molecular weight, the keyboard entry
option is best. For a large number of spectra, the KB
option with automatic data transfer is preferred. The
user makes the choice after calling the time sharing
system and may change options repeatedly during a
time-sharing session. Another option which attempts
to find the best overall match is PBM, or probability
based matching. Presently this requires keyboard entry
of the entire spectrum, and its use is limited by this
requirement.
If the automatic transmission KB option is' selected,
the user must run a spectrum abbreviation program on
the mini-computer before calling the MSSS. This
79
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program, which selects the two most abundant ions in
each 14 amu interval, is used as follows:
SELECT MODE: BRVCCP
STORAGE FILE: SELECT A NAME FOR
YOUR ABBREVIATED SPECTRUM FILE
SPECTRUM FILE: THE NAME OF THE
FILE CONTAINING THE SPECTRA YOU
ARE ABBREVIATING
SPECTRUM NUMBER: 46
BACKGROUND SPECTRUM: 43
MINIMUM VALUE: press return
ANOTHER SPECTRUM: YES or NC)
depending on how many spectra you
are abbreviating
if YES cycle will repeat enabling you to put a
number of abbreviated spectra in one file
if NO the prompt will be ANOTHER FILE?
which enables you to abbreviate spectra
from another data file stored on the same
disk.
If NO again system returns to SELECT MODE:
After generation of the abbreviated spectrum file
another program is used to transmit the data. This
program, named MDIREK, uses the Tektronix 4010
or 4012 or 4014 communications interface and will not
work with the Digital Equipment Corporation KL8E
communications interface. The BAUD rate may be
110-9600 and the program will work with any rate
your modem handles and the time sharing system
supports. The program is used as follows:
SELECT MODE: MDIREK
SPECTRAL DATA COMMUNICATION
PROGRAM
FILE?: NAME OF STORAGE FILE
SELECTED ABOVE.
Place the communications interface three position
switch in the middle position, select a BAUD rate, full
duplex, and call the time sharing system.
The standard login procedure is used and a KB is given
in answer to OPTION?:
OPTION?: KB
COMPLETE SPECTRUM SEARCH
MAIN FILE(Y OR N)? Y_
INPUT TWO TITLE LINES FIRST*"
Place the switch in bottom position and enter two
contol P's followed by a control A. The first control P
causes the file name, spectrum number, and
background spectrum number to print on the CRT.
The second control P causes the sample title to print
out. Control A halts the PDP-8. Place the switch in the
top position and press continue. At the end of the
spectrum transmission, DATA OK? will be printed. It
is important at this point to place the switch in the
middle position so that the next spectrum to be
transmitted is not disturbed. If the data is acceptable
enter a Yj if not enter a N_and the data may be edited.
Upon completion of the search, the system will
transmit all hits with their similarity indexes. It will
.then prompt with CONTINUE? If the response is NO,
you will exit from the KB search. If the response is
YES, the prompt will be SAME SPECTRUM (Y_or
N). Continue as above and transmit the next
abbreviated spectrum, i.e., if you abbreviated a second
spectrum in the same file you may send it by repeating
the sequence of steps beginning with placement of the
switch in the bottom position.
MINICOMPUTER SEARCH SYSTEMS
An alternative to the large, remote, time sharing
system is the use of a search and match system on the
mini-computer of a GC/MS data system. Several data
system manufacturers offer this kind of system and its
use may offer important time and cost savings. The
most serious limitations of local database searching are
the size of the database, the quality of the database, the
difficulty of updating the database, and the very limited
searching capability usually offered with these systems.
The EPA minicomputer search system operates as
an integral part of the PDP-8 GC/MS system software.
The hardware required to use this system is a PDP-8
with 8K of core memory, an extended arithmetic
element (EAE), two disk drives, and a printer such as a
teletypewriter, Decwriter, or line printer. An
alternative search program operates in 16K and
reduces search time by about 5-10 seconds per search.
This is recommended for searching very large numbers
of spectra, e.g, to match 100 spectra in 8K requires
about 17 minutes longer than matching 100 spectra in
16K.
The files required to use this system are not all listed
in the disk directory even though one or more of them
may be present. In addition, some files are write
protected so they are less likely to be clobbered by a
user error. Finally, it is required that certain files be on
certain disks in specific drive units, or all will fail. The
files required and their directory status, write
80
-------
protection status, and disk requirements are listed
below.
BMATCH and BMNBVT. These files should be
copied on all disks that may be used to store data files.
They are conventional directory listed files that are not
write protected. The program BMATCH is used for
spectrum abbreviation and BMNBVT is an overlay.
Spectrum abbreviation is the same function as
accomplished with the program BRVCCP when using
the KB option and the remote search system. However,
its capabilities are significantly enhanced by the
IGOOS software described in section 4.3.
BMN8K and BMN16K. These are the actual search
programs in 8K and 16K versions. They are
conventional directory listed files that are not write
protected. They should be on only one disk, plus a
backup, which is a special skeleton system disk stripped
of the normal data acquisition and data output
software. This skeleton system is initially placed in disk
unit 1, then moved to disk unit 0 after spectrum
abbreviation is finished. The file of abbreviated spectra
is also placed on this disk.
NAMES. This file is very special. It is contained on
the special skeleton system disk, but it will not appear
in the disk directory, and it is write-protected. It
occupies blocks 10000-31277. Therefore, these blocks
are forever inaccessible and any attempt to write
another file into them will result in failure. The number
of.files on the special skeleton system disk must be kept
small and not exceed block 7777. The NAMES file
contains Chemical Abstracts nomenclature for all
compounds in the database, a unique Chemical
Abstracts Registry number for each compound, a
molecular formula, molecular weight, and a purely
arbitrary identification number.
PRNTSP. This is a conventional directory listed file
that is not write-protected. It is on the skeleton system
disk and may be used to print the masses and relative
abundances of abbreviated spectra as they appear in the
database. Please note that the database contains only
abbreviated mass spectra.
PRESEARCH. This is.a special file that is contained
on a disk that has no operating system and cannot be
started with the bootstrap loader. This disk is always
placed in disk unit 1 after the abbreviated spectrum file
is generated on the skeleton system and the skeleton
system is moved to disk drive unit 0. This file contains
the mass of the base peak for each spectrum and other
search algorithm related information. This file is write-
protected.
ABBREVIATED SPECTRUM FILE. This is a
special file that is on the same disk as the
PRESEARCH file, and is write-protected. It contains
mass and abundance data for the two most abundant
ions in each 14 amu window for 25,555 mass spectra.
No two spectra have the same Chemical Abstracts
Registry number.
DATA FILES. When using the search system it is
strongly recommended that the user have descriptive
(up to 64 characters) titles associated with each data
file. Abbreviated spectrum files may contain
information from one or several data files, and
descriptive titles will improve the readability of the
printed report form BMN8K or BMN16K.
Procedure (PDP-8).
1. Place the disk containing the data file(s),
BMATCH, and BMNBVT in disk unit 0. Place the
skeleton operating system in the disk unit 1. Run
BMATCH when both disks are up to speed as
described below using either Q file or keyboard entry
of spectrum numbers. The Q file spectrum number
entry mode is strongly recommended for large
numbers of spectra and is described first:
SELECT MODE: BMATCH
STORAGE FILE? TURKEY
FILE? CINTAP
SPECTRUM? (3
Q-FILE QCIN
FILE? CINTAP
SPECTRUM? (3
Q-FILE? Q2CIN
FILE? 6SPK
SPECTRUM? Q_
Q-FILE? Q26SO
FILE? press return
The storage file is the file that will contain abbreviated
spectra from the data files. Each abbreviated spectrum
requires three disk blocks. The storage file will be
generated on the skeleton system in disk unit 1. The
FILE? prompt refers to the data file on disk 0 that
contains spectra to be abbreviated. A response of Q to
the SPECTRUM? prompt leads to the Q-FILE?
prompt. The user must enter the name of a Q file
created by BCLRGC using the IGOOS described in
section 4.3. This Q file contains a list of spectrum
numbers, and BMATCH will automatically retrieve
each, subtract background if called for, abbreviate the
spectrum, and place the latter in the storage file on disk
unit 1. When the Q file is' exhausted, the program
returns to the SPECTRUM? prompt. The user may
repeat the same process with another data file and the
81
-------
corresponding Q file, or with the same data file and a
different Q file that also refers to the data file. Both
these options are illustrated in the sample dialogue.
Please note that all abbreviated spectra from several
data files \vill be placed in the same storage file on disk
unit 1.
After all spectra from all files have been abbreviated,
the user must press RETURN in response to the FILE?
prompt. If CTRL/L is entered, the program returns to
the system prompt, and all abbreviated spectra will be
lost.
For keyboard entry of spectrum numbers the user
simply enters a spectrum number in place of the Q
command as in the following sample dialogue. If no
background subtraction is required, press RETURN.
SELECT MODE: BMATCH
STORAGE FILE? VOLS
FILE? STD1
SPECTRUM? 56
BACKGROUND? £3
SPECTRUM? 92-
BACKGROUND? 88
SPECTRUM? 1 17
BACKGROUND? 114
SPECTRUM? 127
BACKGROUND 124
SPECTRUM? 192
BACKGROUND? 189
SPECTRUM? 216
BACKGROUND? 212
SPECTRUM? 246
BACKGROUND? 241
SPECTRUM? press return
FILE? press return
SELECT MODE:
It is important to recognize that Q file and keyboard
entry of spectrum numbers may be mixed randomly by
the user and all abbreviated spectra will appear in the
same storage file on disk unit 1. If spectrum numbers
are being entered by the keyboard, the user must press
RETURN twice to return to the system prompt as in
the example above.
2. . Remove both disk cartridges and move the
skeleton system from unit 1 to unit 0. Place the disk
containing the PRESEARCH and 25,555 spectra in
unit 1. Bring both cartridges up to speed.
3. Run BMN8K or BMN16K as shown in the
sample dialogue. The FILE? prompt refers to the
storage file for the abbreviated spectra on the skeleton
system. The user should switch from the CRT to
console printer to allow the printed report to appear on
the printer.
SELECT MODE: BMN16K
FILE? TURKEY
The printed report consists of the title of the file from
which the spectrum was taken, the spectrum number
and background subtracted spectrum (if any), the
number of presearch hits (base peak only in presearch
file), and a list of best hits. For each hit the following is
printed:
a. Similarity index (SI) - see discussion of
similarity index interpretations in this chapter.
b. The Chemical Abstracts name - this
nomenclature system will often generate very long
names for commonly known substances, e.g., dieldrin.
Future versions of the NAMES file will include
common names.
c. The molecular composition - this is printed after
the name.
d. The molecular weight - this is printed after the
composition.
e. The Chemical Abstracts Registry number - this
is a unique number that permanently identifies the
compound. This should be included on all reports of
the occurrence of this compound to allow users of
reports to readily look up the properties of the
compound in other printed or computerized data bases.
f. An arbitrary spectrum identification number
that has no meaning beyond this search system.
A sample report is as follows:
STD #1
SPECTRUM 0056 - 052
47 HITS
SI=0.589
ETHANE, 1,1-DICHLORO-C2H4CL2
75343 # 301
98
SI=0.250
ETHANE, 1-BROMO-2-CHLORO-C2H4BRCL
142 107040 # 1121
81=0.195
CARBONIC DICHLORIDE CCL20
75445 # 307
82
-------
SI=0.153
ETHENE, (METHYLSULFONYL)-C3H6O2S
106 3680022 # 7360
SI=0.135
ETHANE, 1-CHLORO-2-NITRO- C2H4CLNO2
109 625478 # 3569
SI=0.115
ETHANEDIOYL DICHLORIDE C2CL2O2
126 79378 # 460
SI=0.111
PROPANE, 1,1,2-TRICHLORO- C3H5CL3
146 598776 # 3247
When the abbreviated spectrum file is exhausted the
program returns to the system prompt. Clearly this
search system is oriented to processing large numbers
of spectra in an overnight or overlunch batch mode.
One optional program on the skeleton system allows
the user to print mass and abundance data from the
25,555 abbreviated spectra file. The NUMBER?
prompt refers to the arbitrary spectrum identification
number. Pressing RETURN at this prompt causes the
program to return to the system prompt.
measurements were not documented with sufficient
data to support their reliability. This caused doubt
about the validity of the measurements and concern for
the correctness of correlations and proposed standards.
Several aspects of quality control were emphasized in
previous chapters of this manual. Reagent and
glassware control is required to minimize the
introduction of contamination from the materials used
in the sample preparation procedures and this was
emphasized in the sample preparation methods in
chapter 3.
Instrumentation control is required to assure that
the total operating GC/MS system is calibrated and is
in proper working order. If a computerized GC/MS
system is used to collect data, the computer data system
must be included in the performance evaluation. The
recommended instrumentation control procedure was
described in section 2.6. This employs a standard
reference compound and a set of reference criteria to
evaluate the performance of the overall system. This
evaluation should be performed on each day the
GC/MS system is used to acquire data from samples or
reagent blanks. The records from the performance
evaluations should be maintained with the sample and
reagent blank records as permanent documentation
supporting the validity of the data. The major emphasis
of this section is the quality control that applies to
compound identification.
SELECT MODE:
NUMBER? 301
PRNTSP
ETHANE, 1 , 1-DICHLORO- C2H4CL2
98 75343
MASS INT MASS
14 1 15
61 6 63
105 1
NUMBER?
INT MASS
1 26
100 65
INT MASS
6 27
31 83
INT MASS
40 35
14 85
INT MASS
1 47
9 98
INT MASS
1 60
10 100
INT
1
7
5.3 QUALITY CONTROL IN
COMPOUND IDENTIFICATION
The importance of analytical quality control in
organic pollutant analysis cannot be overestimated.
Data generated in surveys are being used to set
standards for drinking water, air quality, surface water
quality, and effluents. Possible correlations between the
presence of organic contaminants in drinking water
and air and human health effects are under widespread
study. In the past many carefully conducted
EVALUATION OF BLANKS AND
REAGENT BLANKS
The blank is an experiment that is required for all
samples. A reagent blank is defined as an experiment
that employs all procedures, quantities of materials,
glassware, etc. used in the sample preparation except
that no water, air, tissue, or sediment sample is used. A
low organic water blank is recommended in place of a
reagent blank in several procedures, e.g., inert gas
purging and trapping. One of these blanks is required
even when contamination from glassware and reagents
83
-------
is well controlled. The data from the blank is the
documentation that proves that good control was
exercised, and it defines the level of background that
was beyond control. The evaluation may be a straight
forward comparison of corresponding peaks and mass
spectra in the blank and sample.
An effective but rapid technique for comparison of
blanks and samples employs the extracted ion current
profile (EICP) of one or several ions. An EICP is
defined as a plot of the change in relative abundance of
one or several ions as a function of time. The data for
this plot is extracted from all the ion abundance
measurements made over the mass range observed
during the elution of the separated components from
the GC. The EICP produces an apparent increase in
sensitivity by subtracting from the total ion current
profile all the ion abundance data that is contributed
from background, unresolved components, and other
irrelevant ions. The EICP generator is a standard data
reduction program on all modern computerized
GC/MS systems and is described in chapter 4 and
section 6.1. A fast graphics display device (CRT) is
required to facilitate reviewing a large number of EICP
plots.
It is emphasized that it is not necessary to have even
a tentative identification of a compound to apply this
technique to blank evaluation. To conduct an EICP
comparison, mass spectra of all peaks in the sample are
examined. One or several ions that are prominent in a
spectrum from each peak are selected, and sample and
reagent blank EICP's are generated on the CRT. In
most cases comparison of these EICP's permits
straightforward judgments concerning the presence of
compounds in the sample and the blank. Figure 5.1
shows EICP's for mass 171 from a sample and from the
corresponding reagent blank. Clearly a compound
having a mass 171 ion is present in the sample, but no
corresponding peak is observed above the noise level in
the reagent blank. Figure 5.2 shows a sample,and
reagent blank that contain the same compounds by
EICP analysis. For a valid comparison this technique
does require exactly the same GC and data collection
conditions for the sample and blank. It is possible that
the compounds in the blank and sample that elute at
the same time are different, but contain the same ion or
ions. If this is suspected, the entire spectrum from each
must be examined to confirm or deny this possibility.
If the concentration of a blank component equals or
exceeds the concentration of sample component, the
decision is clear and the compound must not be
reported. A far more difficult judgment must be made
when the concentration of a sample component exceeds
its concentration in the blank. The material could, of
course, be a true sample component. Alternatively it
has been observed empirically that compounds in the
blank sometimes merely appear to be at lower
concentrations than the same compounds in the
corresponding sample. Figure 5.3 shows the total ion
current profiles from a sample and a corresponding
reagent blank. Careful comparison of the profiles
reveals a very similar pattern of peaks and valleys in
certain areas, e.g., spectrum numbers 170-190 and
235-245, yet a significantly lower apparent
concentration in the reagent blank. There are several
possible reasons for this. One rationalization used, in
the case of solvent extracts, is that impurities in the
solvent of the reagent blank are adsorbed more
efficiently onto the drying agent and other surfaces.
With extracts containing some water, the wetting effect
of the water precludes efficient adsorption on surfaces,
and impurities are carried on in the solvent.
Alternatively, certain solvent impurities may be lost
more readily from the blank than from the sample
extract during concentration. Perhaps the general
organic background matrix in the sample extract
retains the solvent impurities. Both explanations are
reasonable but unproved. In view of the uncertainties,
any compound that is observed in the sample should
not be reported if it is part of an overall pattern of peaks
that is repeated in the blank, although at a lower
apparent concentration. This same overall pattern will
usually persist in the acid, neutral, and basic fractions
of a solvent extract.
SUPPORTING EXPERIMENTS
Chemical ionization, field ionization, and high
accuracy mass measurements are GC/MS techniques
that are capable of generating very strong evidence in
support of identifications. Some of these are discussed
in Chapter 6. However, the production of this evidence
is restricted because only a relatively few laboratories
have developed capabilities with these techniques. High
accuracy mass measurements are further limited by
sample size, since some sacrifice in sensitivity is
required to achieve the high accuracy.
After a tentative identification is made, several other
types of supporting experiments become possible.
Retention time data from the GC/MS of a pure
compound (standard) may be compared with
analogous data from the sample component. Similarly.
the mass spectrum of the standard, obtained under the
same conditions that were used for the sample, may be
compared with the sample component spectrum. The
standard may be dissolved in water at an appropriate
84
-------
oo
en
s?.
8.
p.
8.
L
8-
8.
MASS171 IN REAGENT BLANK
MASS 171 IN SAMPLE
10 20 30 10 SO GO 70 80 SO 100 110 130 130 1« 138 ISO 170 ISO 138 TOO ZIO ZZO 230 21O 250 2EO 270 380 Z30 380 310 3ZO 330
Figure 5.1 The extracted ion current profiles for mass 171 from a sample and the corresponding
reagent blank.
-------
MASS 149 IN REAGENT BLANI
I
ID US 30 10 SB
HfffR
70 80 30
MASS 149 IN SAMPLE
"l""'""l""""'l I I l""l'"1 1 1 1 |""I"VI I ~.|i..y...|....l...1 [ I !' I'"; I
JOB 110 120 130 110 ISO 160 170 180 130 200 210 2SO 230 2K3 ZS3 260 Z10 2BO 330 300 310 32O 330 3W 3SO 3EO 370 380 330
Figure 5.2 The extracted ion current profiles for mass 149 from a sample and the corresponding
reagent blank.
-------
8
8-
8.
B.
*.
fc.
8.
»4
REAGENT BLANK
B IB 20 38 « S9 tO 78 to SB 108 1H) ia 138 lie ISO ISO 1TO 1» ISO 2BS 218 228 230 2« 2SB 3SD 2TO 2BO 238 308 3JO 32D 338 310 368 3E8 37B
Figure 5.3 The total ion current profiles from a sample and the corresponding reagent blank.
-------
concentration, isolated, and measured. The recovery of
this spike in the same fraction in which the suspected
component appeared, and the observation of equivalent
mass spectra for the spike and the sample component,
is strong evidence for confirmation of the identification.
REQUIREMENTS FOR PURE
STANDARDS
Clearly the most convincing evidence for an
identification is obtained by the examination of pure
standards corresponding to suspected sample
components. However, the existence of this evidence is
constrained by the availability of the pure standard and
the additional cost and time required to examine it.
Because it is not usually possible to predict which
compounds will be found, some standards will not be
available immediately. There are many very practical
limitations imposed on the development and
maintenance of a large library of pure authentic
standards. Many compounds are obtainable from fine
chemical supply houses, but procurement time is
variable and may extend to weeks or months. Some
compounds are not available from any supplier,
frequently because they are by-products of industrial
processes rather than manufactured products. This
same limitation of standard availability also precludes
calibrated concentration measurements in many cases.
SIMILARITY INDEX INTERPRETATIONS
Because of the problem of standard availability, it is
worthwhile to determine whether reliable
identifications can exist without standards. One
criterion for a reliable identification that might be used
is a quantitative measure of the exactness of match
between an experimental mass spectrum and a
spectrum from the printed literature or a computer
readable database. A similarity index (SI), calculated
on a scale from zero to one, has been described and
used in several computerized mass spectrum matching
systems including the KB option and PDP-8 search
systems described in this chapter. Experience with this
SI indicates that, in general, a value greater than about
four tenths corresponds to a reasonable match between
two mass spectra. A reasonable match often does imply
an identification, but sometimes it does not. Position
isomers and members of homologous series of
compounds often give very similar mass spectra.
Another undetermined number of compounds simply
are not uniquely characterized by their mass spectra.
Figure 5.4 shows the mass spectrum of an unidentified
compound and the spectrum of the compound
chloropicrin, Cl.CNO,. the match is clearly good by
inspection and a1 SI of 0.453 was calculated.
Nevertheless, the unknown whose spectrum is in
Figure 5.4 is not chloropicrin as determined by the gas
chromatographic behavior of the unknown and pure
chloropicrin.
Another problem with identifications based on
empirical spectrum matching is that significant
differences in ion abundance measurements are
sometimes observed when the mass spectrum of a
compound is measured on two different spectrometers.
Some of these differences are probably caused by non-
uniform calibration procedures or by a failure to use an
ion abundance calibration procedure. Different types of
inlet systems also may have significant effects on
relative abundance measurements. A GC or batch inlet
system that is operated in the 100-250C temperature
range may promote temperature dependent
fragmentations and reduce abundances of molecular
and other high mass ions. With a well designed direct
inlet system, these temperature effects may be largely
precluded. As a result of these factors, it is quite
common for two spectra of the same compound, that
were measured with different inlet systems or
spectrometers, to give a rather low SI. A low SI may
also be caused by unresolved or; partly resolved
components which generate mass spectra containing
extraneous ion abundance measurements.
It is concluded that the SI must be used with caution.
A relatively high SI may be regarded as an indication of
a reasonable match, but only as suggestive of the
probability of an identification. A relatively low SI
cannot be regarded as complete rejection of a possible
identification.
THE QUALITY INDEX
Another criterion for reliable identifications when
standards are not available is based on an assessment of
the quality of the ions in the experimental and reference
mass spectra. In the SI calculation, molecular ions
(M+), molecular ions having naturally occuring
isotopes (typically M + 1, Cl, S, etc.) and all key
fragment ions are weighted the same as many very
common fragment ions. However, the M* ion, for
example, is unique in every mass spectrum and has
significance to an identification that far outweighs most
other ions. Mass spectra may be categorized according
to the quality of the ions observed and a quality index
(QI) calculated that is a weighted similarity index.
QI = SI * W
-------
8
8
JS-
SPECTRJi NLfER 161 - 1S3
C1NC!N*TT! NElfTRFL
SJ
o
Juu
8
20 30 « SO 60 70 90 30 100 110 120 130 110 ISO ISO 170 190
M/ E
STf^CPPD
S_
*8_
rf
5
...,.,..|...,,....|....|....|....1,...|....,....|,...,....J ,....|..n,r,..|....,....|T..^nnj ....... .|....,T. ..|. ........j. ...,..j.. ..,,.!.., |. ......
20 30 10 SO 60 70 80 30 100 110 133 130 11O ISO 160 170 180 130
Figure 5.4 The mass spectrum of an unidentified compound and the mass spectrum of chloropicrin.
89
-------
:veral categories of quality are as follows:
(a) If the molecular ion is observed and the
observed distribution of abundances for it and
its isotope containing species are within 10%
of the expected distribution, the W is 1.0. The
significance of the SI value is considerably
enhanced.
(b) If a molecular ion is observed but the isotope
data are not within 10% of the expected value,
lower confidence is assigned by a W of 0.75.
(c) Failure to observe a molecular ion but the
observation of key fragments that account for
all the atoms of the molecular ion suggests a W
of 0.5. This factor may be raised or lowered
between 0.4-0.6 depending on the observation
of consistent isotope data in the key fragment
ions.
(d) The lowest confidence is placed on spectra
which do not contain adequate fragment ions
to account for all the atoms of the molecular
ion. A W of 0.1 is assigned to these spectra.
It is recognized that position isomers may not be
distinguishable under any circumstances, but this is
often true even when pure standards are available.
The quality index is amenable to additional positive
adjustments by 0.1-0.2 QI units if all major fragment
ions are scrutinized and found to be reasonable and
compatible with the assigned structure.
Reasonableness should be based on compatibility with
the accepted principles of fragmentation of organic ions-
in the gas phase. With magnetic deflection
spectrometers additional fractional quality points may-
be added if fragmentations are supported by the
observation of ions from the decomposition of
metastable ions.
Good spectrum matches that have a QI of 0.75-1.0
are considered reliable identifications when pure
standards are not available.
90
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CHAPTER 6
ADVANCED ANALYTICAL TECHNIQUES
The purpose of this chapter is to describe several
GC/MS techniques that are of a more specialized
nature than the broad spectrum methods described in
the first five chapters. Each of these specialized
techniques has achieved prominence in mass
spectrometry, and each is expected to become more
important in future applications of GC/MS.
Selected ion monitoring is a real time technique
whose operational philosophy differs sharply from the
broad spectrum approach emphasized in the previous
chapters. Unlike the broad spectrum approach,
selected ion monitoring requires knowledge of the
compounds that are to be measured. In a very real sense
it is the application of a mass spectrometer as a super
selective and sensitive GC detector. Its selectivity far
exceeds any known GC detector, and its sensitivity is at
least the equal of the most sensitive detectors known.
The technique is discussed in section 6.1.
During the last fifteen years the emphasis placed on
qualitative analysis by mass spectrometry has
somewhat obscured the quantitative analytical
strengths of the technique. Today quantitative analysis
by mass spectrometry is more significant than ever,
especially when used with selected ion monitoring.
Quantitative analytical methods are discussed in
section 6.2.
The development of open tubular column GC
technology is expected to be very significant during the
next five years, and reliable, long lasting precoated
columns will likely be available at relatively low cost
from a variety of suppliers. This technique is changing
so rapidly that section 6.3 is devoted largely to a
presentation of a few basic principles, and to a
discussion of several potential areas of application.
Chemical ionization GC/MS is discussed in section
6.4, and because of the very broad scope of this
relatively new technique, the presentation is limited to
a few basic principles, quality control considerations,
and environmental applications.
Precise mass measurements are currently beyond the
capabilities of most environmental GC/MS
laboratories. The brief discussion of this technique is
included in section 6.5 primarily for the information of
readers who should be aware of the capabilities that
exist, and the advantages and disadvantages of the
method.
6.1 SELECTED ION MONITORING
(SIM)
The computer controlled mass spectrometer has two
general modes of operation as a continuous detector in
chromatographic systems. One mode is to acquire
conventional mass spectra of components as they
emerge from the chromatographic system. These mass
spectra are used to identify the individual components.
This broad spectrum approach was emphasized in the
first five chapters of this manual.
The alternative mode is to apply the mass
spectrometer as a substance selective detector. This
mode is called selected ion monitoring (SIM) which is
defined as the dedication of a mass spectrometer to the
acquisition of ion abundance data at only selected
masses in real time as components emerge from the
chromatographic system.
Selected ion monitoring is not a new principle in
mass spectrometry. A technique called peak stepping
or peak switching has been used for decades in the
precise measurement of isotope ratios. In this classical
application, the ionic abundances measured were
usually limited to those separated by just a few atomic
mass units, for example "0 and "0. In recent years there
has been a very significant increase in the applications
of SIM. This was brought about largely by the
development of the computer controlled quadrupole
mass spectrometer as vapor phase chromatography
detector. The presence of the gas chromatography inlet
system permitted tn'e introduction into the mass
spectometer of very small samples of complex mixtures
in an easily handled liquid form. The computer
91
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controlled quadrupole mass spectrometer provided a
method for high speed and very accurate and precise
ion monitoring over a very wide mass range. Finally the
dedicated minicomputer and its related peripherals
gave Uie. experimentalist, access to a wide range of
control functions and real time ion monitoring
techniques.
DEFINITIONS OF TERMS
There is usually a period of confusion in
terminology, concepts, etc. any time that technology is
rapidly advanced by a number of individuals and
organizations in a relatively short time period. The
application of a mass spectrometer as a substance
selective detector in chromatography is no exception.
The terms accelerating voltage alternation, mass
fragmentography, single ion detection, and multiple
single ion detection are among a number of terms that
have been used to describe this technique. An analysis
of this terminology led to the recommendation of a
standard term, selected ion monitoring (SIM), because
it best conveys to the reader the significant information
about the technique that sets it apart from other
techniques. The term SIM is general in that it does not
imply a particular type of spectrometer, the number of
ions measured, or the type of ions measured. It must be
recognized however that SIM is a real time
measurement technique and that a designation is also
required for the output obtained from SIM. The name
selected ion current profile (SICP) has been
recommended as the most meaningful and appropriate.
Consistent with the definition of SIM, a SICP is then a
plot of the change in ion abundance as a function of
time using abundances measured by SIM.
Clear precise terminology is particularly important
in computerized GC/MS work because there are
several other widely used techniques that may be
confused with SIM and the SICP. It is important to
understand these techniques to appreciate the overall
advantages and disadvantages of SIM. Perhaps the
most widely used real time data acquisition technique
in GC/MS is the continuous repetitive measurement of
spectra (CRMS). Figure 6.1 contains a schematic
diagram of CRMS and two types of data reduction that
are in common use. The sawtooth diagram in the top of
Figure 6.1 is a representation of CRMS during the
elution of components from a gas chromatograph.
Each solid line represents a sweep of the mass
spectrometer Trom an arbitrary starting mass, e.g., 40
amu, to an arbitrary ending mass, e.g., 400 amu. Each
dotted line represents the resetting of the mass
spectrometer sweep control to the starting mass. In a
typical GC/MS run, several hundred to over a
thousand mass spectra may be acquired in this way.
Each sweep of the mass range usually requires a time in
the range of 2-5 seconds, but faster or slower scans may-
be used in some cases. The second diagram from the top
in Figure 6.1 merely shows that each solid line of the
sawtooth represents a mass spectrum as displayed in
the standard histogram format. The most important
idea is that CRMS produces a set of mass spectra that
are more or less complete depending on the selection of
the mass range. Each integer mass between the starting
and ending masses is measured and recorded. This is in
sharp contrast to SIM where measurements are made
at only a few masses in real time.
The third diagram from the top in Figure 6.1
illustrates a 'widely used data reduction process that
uses data acquired by CRMS. Each point on the
ordinate is the normalized sum of all the ion abundance
data in a single mass spectrum and, each point on the
abscissa represents the spectrum number or a
corresponding unit of time. This plot is referred to as a
total ion current profile (TICP) which is defined as a
normalized plot of the sum of the ion abundance
measurements in each member of a series of mass
spectra as a function of the serially indexed spectrum
number. This same plot is often referred to as a
reconstructed gas chromatogram (RGC), but this
nomenclature is not preferred as it does not accurately
define a TICP. An RGC could just as well be the
output of a flame ionization detector, as redrawn by a
draftsman. An important point to recognize is that the
TICP in Figure 6.1 is the result of a computer data
reduction and not real time display. With magnetic
deflection spectrometers it is common to continuously
monitor the unresolved ion beam and produce a total
ion current plot in real time. This plot should be similar
to the TICP in Figure 6.1, but clearly it will differ in
that it will contain contributions from ions below mass
40 and above mass 400.
There is one more very valuable data reduction
technique whose output is most often confused with a
SICP. In this technique data acquired by CRMS, and
perhaps displayed in a TICP, is further reduced by
plotting the change in relative abundance of one or
several ions'as a function of time. This plot is illustrated
at the bottom of Figure 6.1. The plot appears very
similar to a SICP but the data used are quite different.
The significance of this difference is explained below,
but first a clear precise name for this output is required.
The original name suggested was mass chromatogram.
Unfortunately this is not a very descriptive name and it
may be confused with the output from a gas density gas
92
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400 AMU (2-
40 AMU (0 SEC)
\
100
RELATIVE
ION
ABUNDANCE
o
,
L
MASS, AMU
REL.
TOTAL
ION
ABUN
', .»
V TICP
*','"'.
SPECTRUM NUMBER (TIME)
REL.
PART.
ION
* X
EICP
TIME (SN)
Figure 6.1 A schematic diagram of continuous repetitive measurement of spectra, a TICP, and an EICP.
93
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chromatographic detector. The name extracted ion
current profile (EICP) is more meaningful because the
data for the few ions used in the plot are extracted from
the larger set used to generate a TICP. The terms
limited mass output or limited mass search are often
used to describe this same plot. However they are less
meaningful than EICP since the nature of a limited
mass is not clear.
The significant difference between a SICP and a
EICP is that SIM produces a real increase in
signal/noise by time averaging random noise. The
EICP produces an apparent increase in sensitivity by
removing from the TICP the ion abundance data from
background, unresolved components, and other
irrelevant ions. The contrast between continuous
repetitive measurement of spectra and SIM is
illustrated in Figure 6.2. If the sweep of the complete
spectrum is made in 3.6 sec (3600 millisec) then the
data system may integrate the ion current at each
integer mass for 10 msec (3600 msec/360 amu). If the
same total time is allowed for all the measurements at
each of the selected masses 99, 157, 203, and 250 amu
in real time, then integration of signal intensity at each
may proceed for 900 msec (3600 msec/4 amu). The
longer integration time during SIM permits
enhancement of the signal to noise ratio by averaging of
random noise. Therefore there- is a substantial
improvement in the detection limit by SIM.'This.is in
contrast to the EICP which still uses the 10 msec data
with its inherently lower signal/noise.
The SICP illustrated in the third diagram from the
top of Figure 6.2 was generated by summing the
abundances of all four ions measured during SIM.
Clearly one could also plot the change in abundance of
each ion separately and we make no distinction
between various types of SICP plots. However, as
illustrated in the bottom of Figure 6.2, a SICP for mass
125 would yield no peak since mass 125 was not
measured during SIM.
Figure 6.3 is a display of a TICP, SICP, and an
EICP. The TICP was generated from CRMS over the
40-400 amu mass range during chromatography of
seven chlorobiphenyl isomers. Five nanograms of each
isomer was injected and an 11 msec integration time
was applied at each mass. The total time for a 40-400
amu sweep was about 5 sec. The EICP was obtained
from the TICP using seven masses characteristic of
chlorobiphenyls. The SICP is the result of SIM using
the same seven masses, but an integration time of 540
msec on each. The SICP is the sum of the data from the
seven masses. The signal to noise contrast between the
SICP and EICP is clearly demonstrated. This
illustration is not meant to imply that EICP is not.
valuable technique, but to show .the differences in the
methodoloy.
A routine application of an EICP is shown in Figure
4.3. In this example the. TICP data has an adequate
signal/noise and the EICP was used, to effectively to
highlight those areas of the chromatogram having
abundant mass 149 measurements.
SELECTION OF MASSES
The principle potential advantages of selected ion
monitoring may be.summarized as follows:
1. High Selectivity
2. Tunable Selectivity
3. Qualitative Reliability
4. High Sensitivity
5. Reduced Need for Sample Purification
6. Quantitative Accuracy
In practice it may not be possible to. achieve all of the
advantages simultaneously. There is a general tendency
to select the most abundant ion or ions in a spectrum in
order to optimize sensitivity. In certain cases this may
have a significant effect on, the selectivity, and therefore
the reliability of the measurement. For, example, the
most abundant ion in. the, electron, ionization spectrum
of 2-methylbenzothiazole is the molecular ion, mass
149. However selection, of this ion for SIM could result
in measurement errors due.to the ubiquitous phthalate
esters which dis,play intense mass 14.9, fragment ions.
The selection of a. less abundant but more selective ion
may provide adequate detection limits and preserve the
reliability of the measurement.
One method of selecting, masses is to employ a
computerized mass spectral search system (chapter 5)
to evaluate the selectivity of candidate masses in, the
spectrum of the compound of interest. In this method,
the frequency of occurrence of several candidate
masses in a large, data base of mass spectra is
determined, and the results are used to select a mass or
masses having an acceptable trade-off between
selectivity and sensitivity.
A method of maintaining qualitative reliability is to
monitor several ions from the same compound that
have an established abundance relationship. The
molecular ion and its corresponding isotope containing
species have abundance relationships that are well
known. If the compound of interest contains chlorine,
bromine, or other elements with several abundant
isotopes, an excellent approach to qualitative reliability
is to monitor several ions and compare the observed
94
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400AMU (2-5SEC)
CRMS
40AMU(OSEC)
SIM
/ / 250
' / 203
' 157
/ 99AMU
REL
PART.
ION
ABUN
V
X
REL
PART.
ION
ABUN
\ SICP
X
x*
v TIME(SN)
SICP
TIME (SN)
Figure 6.2 A schematic diagram of continuous repetitive measurement of spectra, SIM, and two SICP's
95
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CHLOROBJPHENYLS
0 10 ZO 30
9aECTRLM NU"BER
SO 'GO 70 80 90 100 110 120 130 HO ISO 160 170 183 130 200 210 220
Figure 6.3 A TICP, SICP, and EICP from the chromatography of seven chlorobiphenyl isomers.
-------
and expected abundance ratios. Figure 6.4 shows a
number of calculated chlorine/bromine isotope
distribution patterns normalized to the most abundant
ion of the group. Within these patterns are numerous
possibilities for comparisons of ratios. For compounds
that do not contain readily measurable isotopic species,
it ,is recommended that several ions of experimentally
determined relative abundance be monitored and their
abundance ratios compared.
If several ions from the same compound are
monitored, selectivity may be improved significantly by
a data reduction program that plots a sum of the
abundances of the selected ions at a spectrum number if
and only if all the selected ions are above a defined
threshold. The advantages of this technique will be
more generally recognized as programs. with this
capability are developed.
The reduction in sample preparation as a result of
SIM will depend on the nature of the sample. In the
environmental field, air and relatively clean water
samples offer the best possibility for elimination of all
extract purification. For fatty tissue, sediment, and
sewage samples some reduction in extract purification
is usually possible.
One difficulty with SIM is the simultaneous
measurement of two or more components with
significantly different concentrations. Selection of a
long integration time will enhance the signal/noise of
less abundant ions, but abundant ions will saturate the
detection system. Alternatively, a short integration
time may avoid saturation of the detector but preclude
clear observation of the less abundant ions. A partial
solution to this problem is a method for the dynamic
selection of integration time as a function of signal
strength (IFSS), as described in chapter 2.
SIM USING THE CONTROL PROGRAM
In section 2.7, the control program options were
described and the possibility of using this program for
selected ion monitoring was implied. However all
previous examples of the application of this program in
this manual demonstrated the program with
conventional wide mass range data acquisition. In
place of entering a single mass range in response to the
MASS RANGE? prompt, the user may enter up to 8
individual masses separated by semicolons or a mixture
of up to 8 individual masses and mass ranges separated
by semicolons. The masses and/or mass ranges must be
entered in ascending, non-overlapping order and they
need not be contiguous.
If more than one mass or mass range is entered, a
corresponding number of integration times and
samples/amu must be entered separated by.semicolons.
These have the same meaning as described in section
2.7. The following sample dialogue illustrates selected
ion monitoring with the control mode using eight ions
characteristic of chlorinated biphenyl compounds;
SELECT MODE: CONT
CALIBRATE?: N_
TITLE: SIM FOR PCB'S USING 8 IONS
CALIBRATION FILE NAME: CAL
FILE NAME: SIM
MASS RANGE: 190;224;260;294;330:
362;394;426
INTEGRATION TIME: 400;400;400;400:
400;400;400;400
SAMPLES/AMU:
THRESHOLD:
RT ON CRT?:
RT GC ATTEN: 5
1; 1; 1; 1; 1; 1; 1; 1
H
MS RANGE SETTING?: _
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?
The ions used in this example are selective for
chlorobiphenyl compounds with different levels of
chlorination and do not give optimum sensitivity. The
.choice of 400 milliseconds as an integration time is an
example of the use of SIM to signal average random
noise for a significant improvement in the signal to
noise ratio. It also embodies the idea of choosing an
integration time such that a complete cycle through the
selected masses requires about the same overall time as
a conventional data acquisition from 33-450 amu using
CRMS. Under these conditions the spectrum number
index displayed on the SICP will be approximately the
same as the spectrum number index displayed on the
TICP.
The advantages of using the control program for
SIM include the ability to output the results using the
standard output programs described in section 4.1 and
MSSOUT described in section 4.2. Output as a TICP
will produce a SICP which displays the sum of the
abundances of the selected ions as a function of time.
Individual masses may be displayed using the EICP
capability. Another significant advantage is the IFSS
capability as defined in section 2.7. Sample dialogue for
SIM with IFSS is as follows:
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: SIM FOR PCB'S USING 8 IONS
97
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8.
vo
CO
B.
o
O-
CIBr3 CI2Br3 CI3Br3 CI4Br3 CIBr4 CI2Br4
Br,
Br3
Br,
_s
.W
.8
IP
_B
Figure 6.4 Some calculated chlorine-bromine isotope distribution patterns.
-------
CALIBRATION FILE NAME: CAL
FILE NAME: SIM
MASS RANGE: 190;224;260;294;330;
362;394;426
SAMPLES/AMU: 1;1;1;1;1;1;1;1
SCALE FACTOR: K)
TITLE: SIM TEST
MAX RPT COUNT: j_6
, BASE INTEGRATION TIME: j_
RPT COUNT BEFORE CHECKING LOWER
THRESHOLD: 4_
LOWER THRESHOLD: 2_
UPPER THRESHOLD: 2_
RT ON CRT?:
RT GC ATTEN: 5_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?
For each mass or mass range selected a sample/amu
value must be entered. A single entry is acceptable for
the base integration time and the other IFSS
parameters. However one may enter a string of values
separated by semicolons for IFSS parameters and these
will be applied to the masses or mass ranges in the usual
way.
SPECIALIZED SIM PROGRAMS
There are several data acquisition and data output
programs that are specifically for selected ion
monitoring, and cannot be used for more generalized
types of data acquisition or data output. However these
programs have several advantages that may favor their
use in certain applications. The data acquisition
programs have a digital integration feature which may
be used to improve signal/noise with very low level
signals. The data display programs have a digital
smoothing feature to further improve signal/noise, and
the plotter display program allows the user to exactly
overlay selected ion current profiles of two or more
ions.
The data acquisition programs are named CRTSIM
and PLTSIM. The programs are the same except that
CRTSIM creates the real time display on the CRT
screen, and PLTSIM creates the real time display on
the plotter. The dialogue for the two programs is the
same:
SELECT MODE: CRTSIM OR PLTSIM
CALIBRATION FILE: CAL7
MASS(ES): 198,442,443
-'INTEGRA. TIME: 50
NO. POINTS: J_0
RUN TIME: 30
DATA FILE NAME:
DATA
DFTPP
In response to the MASS(ES): prompt the user may
enter from one to eight masses separated by commas. It
is possible to enter fractional masses such as 440.3. An
integration time from 1 to 4096 msec may be specified
for each mass entered, or a single time may be entered
which applies to all the masses. If the number of
integration times entered is less than the number of
masses, the last time entered will be used for the masses
which had no integration time specified. The number of
points is the number of times each mass is integrated
before a combined value is stored in the data file. The
run time is entered in minutes, and the scale factor is an
integer amplification factor for the real time data
display. During data acquisition three commands are
acceptable with the following results:
CTRL/L terminates data acquisition, saves the data
file, and returns to the monitor
£ terminates data acquisition, deletes the data file, and
returns to the monitor
Fn (where n=an integer) changes the scale factor in
real time, but does not affect the data already stored
in the data file.
The data files created by the two data acquisition
programs are compatible with the two data output
programs named CRSMPT and PTSMPT. The data
files are not compatible with the output programs
described in chapter 4 (however see CONVRT below).
Furthermore the CRSMPT and PTSMPT programs
cannot output data generated by the control program
in either the control or IFSS modes. Sample dialogue
for CRSMPT is as follows;
SELECT MODE:
FILE? PFTBA
FIRST MASS?
CRSMPT
219
SECOND MASS? 502
INDIVIDUAL NORMALIZATION? Y_
This program plots digitally smoothed selected ion
current profiles for two ions on the CRT. Only the first
200 data points are displayed for each ion. By pressing
any key, the next 200 data points are displayed and this
procedure may be continued until all data points have
99
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been plotted. The program then returns to the FIRST
MASS? prompt. A Y_ response to the INDIVIDUAL
NORMALIZATION? prompt will cause each profile
to be normalized on the largest peak in each individual
profile. Any response except Y_ will cause all the
profiles to be normalized on the largest peak in the
entire data file.
Digital smoothing causes actual plotting to begin at
the seventh data point and terminate six data points
before the last point in the file. The smoothing may
result in the most intense peak for any ion being a few
percent too large or small. A CTRL/L command
returns-the user to the system monitor.
The dialogue for the plotter program PTSMPT is as
follows:
SELECT MODE: PTSMPT
FILE? PFTBA
MASS? 219
SMOOTH? Y_
INDIVIDUAL NORMALIZATION: Y_
OVERLAY? Y_
MASS? 502
SMOOTH? Y_
INDIVIDUAL NORMALIZATION? Y_
OVERLAY? N_
MASS? 503
SMOOTH? Y_
INDIVIDUAL NORMALIZATION? N_
OVERLAY?
This program is somewhat different in that only one
profile is plotted and then the user has an option of
either overlaying one or more profiles (perhaps using a
different color ink) or plotting the additional profiles
separately. The actual plotting begins immediately
after the INDIVIDUAL NORMALIZATION?
prompt which has the same meaning as in CRSMPT.
Also, the user has the option of omitting the digital
smoothing routine. Again the CTRL/L command
returns the user to the monitor.
There is a program that converts CRTSIM or
PLTSIM data files into files compatible with the output
programs described in chapter 4. The program is called
CONVRT and is run as follows:
SELECT MODE: CONVRT
FROM UNIT: O_
INPUT FILE: TEST
TO UNIT: O_
OUTPUT FILE: CTEST
SIMEXC (12K and EAE required) and CRTSM2 (an
overlay) expand the capabilities of CRTSIM by
allowing an unlimited number of mass sets to be
monitored one at a time, with each set containing up to
8 masses. The mass sets entered, ^together with
integration times are withdrawn sequentially, so that
users should enter these on the basis of retention time.
The user only calls SIMEXC, never CRTSM2, and
SIMEXC controls all data flow and program control.
After calling SIMEXC, the dialogue is exactly like
CRTSIM, except after all information is input for a set
of masses the question MORE INPUT? is asked, to
which the user should respond Y if additional sets of
masses are to be entered. Any other response is treated
as a negative one, resulting in the printing of DATA on
the screen. One pitfall must be pointed out so that it can
be avoided. A different file name is required for data
storage for each set of masses. SIMEXC tests for
duplicate file names among catalogued files, but does
not test for duplicate entries within its own dialogue.
This can result in a halt in the program overlay
CRTSM2 if duplicate names are entered in SIMEXC.
SIMEXC-CRTSM2 detects the presence of a saturated
peak during data acquisition. At the time a file is
catalogued, it prints SATURATED PEAK on the
screen and halts, forcing action by the operator. To
continue the run, the CONTINUE switch on the
computer must be depressed. Mass sets may be
changed in two ways. First, after the run time for a
given set has expired, the next set is automatically
withdrawn and data acquisition begins for that
following cataloging of the previous file. Secondly,
striking CTRL-L during data acquisition automatically
halts acquisition on the current set, cataloging of the
file, and initialization of the next set.
6.2 QUANTITATIVE MEASURE-
MENTS
There are several important advantages gained by
making concentration measurements by GC/MS.
Quantitation with selected ion monitoring is widely
used because it offers the ultimate in compound tunable
selectivity, high sensitivity, precision and accuracy.
Indeed the ultimate in quantitative accuracy is possible
with SIM and a stable isotope labeled internal
concentration calibration standard that is the same
compound as the measured analyte. Because of the
high selectivity of SIM, some reduction in sample
purification is usually possible and this adds cost-
100
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effectiveness to the approach. The use of data obtained
by continuous repetitive measurement of spectra for
quantitative analysis will clearly result in less
sensitivity and pernaps lower accuracy and precision..
However, the same tunable selectivity is available
through the extracted ion current profile, and
significant cost effectiveness is possible by use of the
same data file for both qualitative and quantitative
analyses.
There are a very large number of procedures for
quantitative measurements with GC/MS. These range
from standard manual measurements of peak heights
or areas in the plotter display of the real time total ion
chromatogram, to off line computations using digital
data printed with the Adoption of the standard output
program. Measurement of peak heights is particularly
effective with data acquired by the SIM programs
CRTSIM or PLTSIM and displayed with the program
PTSMPT.
Manual methods are not discussed further in this.
section since these are generally understood by
individuals experienced in chromatography work, and
many authors have written on the subject. The purpose
of this section is to define a number of terms used in
quantitative analysis, to present some general
guidelines for use of concentration standards, and to
document the application of three programs to
quantitative measurements. The programs are named
QNTSET/QNTATE. QUANX (where x = a revision
number,) and the IN option of MSSOUT. The
MSSOUT software is described fully in section 4.2, and
the user should consult this first to understand the
basic operations of MSSOUT.
The following terms are defined to assure that all
readers understand the same meanings for several
important terms.
External Concentration Calibration Standard
(ECCS): A known amount of a pure compound that is
measured separately (externally) from identically the
same compound in a sample or sample extract. The
measured detector response from the external standard
is used to calibrate the concentration measurement of
the same compound in the sample.
Internal Concentration Calibration Standard
(ICCS): A known amount of a pure compound that is
added to a sample or sample extract, but is not one of
the compounds found in the sample. This compound
may be labeled with an isotope or isotopes, but usually
is not because it is not found in the sample. The
measured detector response'from the internal standard
is used to calibrate the concentration measurements for
other compounds in the sample or sample extract that
are chemically different. This calibration is
accomplished through independently measured
response factors (RF) for each compound using the
equation below. The independent measurements of
RFs are made with an external standard that also
contains the internal standard.
Area (X)
RF =
Amount (X)
Area (S)
Amount (S)
where: Area (X) =
Amount (X) =
Area (S) =
Amount (S) =
the peak area of the
compound in consistent
units.
the quantity of the
compound injected in
consistent units.
the peak area of the
internal standard in
consistent units.
the quantity of internal
standard injected in
consistent units.
Isotope Labeled Internal Concentration Calibration
Standard (ILICCS): A known amount of a pure
compound that contains a known proportion of an
isotope or isotopes in an amount different from the
naturally occurring amount. This compound is added
to a sample or sample extract that contains the same
compound with a natural distribution of isotopes. This
is a special case of the internal concentration
calibration standard which does not require the use of
response factors. The presence of isotopes does not
generally change a compound's response in a detector,
or its extraction efficiency but the labeled and natural
material may be distinguished with a mass
spectrometer because of the differences in the masses of
labeled ions. However, if the labeled internal standard
were used to quantify chemically different compounds
in the same sample, response factors would be required
as described above.
Spike{s): A known amount of a pure compound that
is added to the original environmental sample, and is
the same compound as found in the original
101
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environmental sample. The measured percent recovery
of the spike is taken as a measure of the accuracy of the
total analytical method with the sample matrix, and
when there is no change in volume due to the spike, it is
calculated with the equation;
P= 100(0-X)/T
where: P = the percent recovery of the spike.
O = the measured value of the concentration
of the analyte in the sample after the spike
is added.
X =the measured value of the concentration
of the analyte in the sample before the the
spike is added.
T = the amount of the spike added expressed
in terms of its concentration in the
sample.
Surrogate Spike (SS): A known amount of a pure
compound that is added to the original environmental
sample, but is not one of the compounds found in the
sample. The measured percent recovery of the
surrogate spike is taken to be indicative of the
recoveries of the compounds in the sample when actual
spikes of each are not used.
Laboratory Control Standard or Check Standard
(LCS): a sample that is prepared in the laboratory by
dissolving a known amount of a pure compound in a
known amount of water or an organic solvent. The final
concentration calculated from the known quantities is
the true value of the standard. The measured percent
recovery of the laboratory control standard is taken as
a measure of the accuracy of the analytical method
independent of various sample matrices.
Duplicate (D): Two aliquots made in the laboratory
of the same environmental sample. Each aliquot is
treated exactly the same throughout the laboratory
analytical method. The difference in the values of the
duplicates is taken as a measure of the precision of the
method.
Regardless of whether internal or external
concentration calibration standards are employed, the
standards and unknowns should be run under identical
conditions in so far as this is possible. Therefore, GC
temperature programming, integration times, and mass
range in control runs or integration times, repeat count,
and number of masses monitored in SIM runs should
be identical to cancel as much error as possible. No
delay between scans should be utilized since it has been
found that better results are obtained on broad peaks as
opposed to rather sharp ones. Also good results are
often far more dependent on the stability of the
instrument sensitivity, baseline zero, and calibration
than on the exactness of the quantitation program.
In general the use of an 'isotope labeled internal
concentration calibration standard for each compound
measured will be precluded because of the
unavailability and/or high cost of such standards. Also
the use of isotope labeled standards in this way requires
fairly complex computations to account for
background ions. These standards are best applied in
specific situations for measurements of one or a few
compounds.
For either internal or external concentration
calibration standards it is necessary to measure the
standards and, for internal standards, revalidate the
response factors on every day that measurements are
made of unknowns in samples. This is because some
GC/MS system drift is inevitable and good results.
depend on system stability as much as any other factor.
The daily measurement of an external standard and/or
revalidation of response factors does not increase
workload since this may be accomplished concurrent
with a required daily measurement of an external
standard to assure proper chromatographic resolution
and system performance.
It should also be established that concentrations are
a linear function of peak areas f6r each compound
measured, and the assumption of linearity should not
extend beyond the established working range. For
sample extracts it is strongly recommended that the
internal concentration calibration standard or
standards be placed in the concentrated sample extract
no more than a few minutes before the measurement.
The purpose of this is to protect the concentration
standard from losses due to evaporation, adsorption, or
chemical reaction. An exception to this is the inert gas
purge and trap procedure, where the internal
concentration calibration standard must be added to
the original sample. With this procedure the total
method, including the purge efficiency, is calibrated
with internal or external standards. However the time
constraint is still present, and the purging should begin
immediately after adding the internal standard. With
isotope labeled internal concentration calibration
standards, the standard is often added to the original
sample to calibrate the total method, including the
extraction efficiency. However this is a dangerous
procedure since the relatively long contact time with
the raw sample may result in losses of the calibrant, and
cause serious errors in the measurement. This type of
calibration should be attempted only if it is established
that the internal standard is stable in the sample
102
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matrix. For internal concentration calibration
standards that are different compounds than the
measured analyte, additional errors may be produced if
the standard is added to the original sample. These
would be caused if the extraction efficiencies of the
standard and measured analytes were different, but the
response factors were determined without taking into
account this difference.
Individual recovery efficiencies should be
determined with spikes into representative samples.
Measured values of unknowns should not be corrected
with the recovery data from a single spike, but the spike
recovery data should be reported to the end user.
Laboratory control standards are used to measure
recoveries independent of sample matrices. Surrogate
spikes may be used as a rough method check.
The final concentration of the unknown in ug/1 is
computed with the equation below when an internal
concentration calibration standard is employed. Areas
and RF are as defined above.
C(X) =
Area (X) * Amount(S)
Area(S) * RF * V
where: C(X) = the concentration of the unknown
in the original sample
micrograms per liter
in
Amount(S).= the quantity of internal
standard added to the concentrated
extract in micrograms
V = the volume of the original sample in
liters.
One of the disadvantages of an internal
concentration calibration standard is that it must be
added to a sample before the general concentration
levels of the unknowns are known. Therefore the
standard may be present in much greater or smaller
quantity than the unknown. This may give rise to
serious errors. External standardization has the
advantage of allowing the concentrations of standards
to be defined after making an estimate of the
concentration levels of the unknowns. Therefore the
standard/unknown . concentration ratios can be
adjusted to a low value which may lead to more
accurate measurements.
With these quidelines, it is feasible to use chemically
reactive compounds, such as anthracene-d,0, for
internal concentration calibration. However, better
choices are available including many brominated and
fluorinated compounds that are not likely to be as
chemically reactive and variable in composition.
Several possibilities exist including 1,4-
dibromobenzene, a tribromobenzene,
pentafluorobromobenzene, or perfluorobenzene.
Although there is very' little published data,
quantitative analysis with continuous repetitive
measurement of spectra and a single external
concentration calibration standard in one laboratory
gave an average bias of -30% for aqueous laboratory
control standards in the 0.1 - 10ug/l range.
All of the programs described are compatible with
the use of internal concentration calibration standards.
This is accomplished by entering the same data file
name for the standard and the unknown. More specific
instructions for internal standards are included in the
description of each program. The QUANX program is
particularly well adapted to internal standards since it
contains an option to enter response factors.
The programs QNTATE and QUANX quantify an
unknown by a simple linear extrapolation from the
peak area measurement of a single standard. Therefore
it is desirable for the concentration of the standard to be
reasonably close to the concentration of the unknown.
A factor of 3 or 4 is considered reasonable but linearity
should be established as described above. The program
MSSOUT does not do this computation, but merely
prints out the integrated peak areas for various peaks
from various files. The user must make the final
calculation and may include a response factor if
desired.
In the sections that describe the individual programs,
the examples were generated from the same two data
files and the results obtained give a direct comparison
of the three programs. The data files were obtained
from 50ng and lOOng injections of DFTPP and are
representative of clean, well resolved, well shaped
peaks. Therefore the results obtained are probably the
best that can be expected from the programs.
MEASUREMENTS WITH
QNTSET/QNTATE
This pair of programs has several advantages. They
may be used with data files acquired under the standard
control mode, IFSS, or one of the specialized SIM
programs CRTSIM or PLTSIM. QNTSET is used to
create a file of peak area data using information from a
data file generated by a concentration standard; and
QNTATE is used to relate standard and unknown peak
areas and print out concentrations in nanograms. A
disadvantage of this pair of programs is that they
cannot be used in the extracted ion current mode, i.e., if
the standards or unknowns were measured with the
control or IFSS mode using a range of mass units, all
103
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the abundances measured at all the masses are used in
the quantitation. There is no provision to extract
abundances at specific masses and use only these for
quantitation. However, if data was acquired with
control, IFSS, CRTSIM, or PLTSIM at a specific mass
or masses, clearly only the specific mass or masses will
be used in the quantitation. Peak areas in both
QNTSET and QNTATE are computed with the
baseline subtracted. The user specifies the spectral
limits of the peak and the program then assumes that
the baseline connects the first spectrum before the
starting value and the first spectrum after the
terminating value.
Sample dialogue for QNTSET is as follows:
SELECT MODE: QNTSET
STANDARDS FILE NAME? STAN
SPECTRUM FILE? REF100
FIRST SPECTRUM? £8
SECOND SPECTRUM? 75
SPECTRUM NUMBER OF MAXIMUM? 1_\.
NAME OF COMPOUND? DFTPP
NANOGRAMS OF COMPOUND? 100
SAME FILE? N_
NEW FILE? N_
The STANDARDS FILE NAME is not a data file
from the GC/MS of the standards, but a new file to be
created by QNTSET that will contain peak area data
from the standards. Therefore a new file must be named
by the user. The SPECTRUM FILE is the name of the
data file from the GC/MS of the standards. The FIRST
SPECTRUM is the first spectrum number of a GC
peak, the SECOND SPECTRUM is the final spectrum
number of the same GC peak, and the SPECTRUM
NUMBER OF MAXIMUM is the spectrum number
from the same GC peak where the total ion abundance
reaches a maximum. The NAME OF THE
COMPOUND may be entered by the user and the
quantity of material expressed in nanograms injected.
This must be expressed as an integer number, e.g., if
one microgram was injected, the user should.enter
1000.
The SAME FILE? prompt should be answered
positively if the user wishes to enter peak area data for
another peak from the same GC/MS data file into the
same peak area file. The NEW FILE? prompt should
be answered positively if the user wishes to enter peak
area data for another peak from a different GC/MS
data file into the same peak area file. A negative
response to this last prompt causes the peak area file to
be closed and saved and the user is returned to the
system prompt. A response of CTRL/L to any prompt
causes the program to abort, and all peak area data will
be lost.
The QNTATE program requires the presence of the
peak area file generated by QNTSET. Sample dialogue
is as follows:
SELECT MODE: QNTATE
SPECTRUM FILE? REF50
FIRST SPECTRUM? 68
SECOND SPECTRUM? IB
SPECTRUM NUMBER OF MAXIMUM? 7_1
STANDARDS FILE NAME? STAN
PEAK NUMBER: j_
DFTPP 54 NANOGRAMS
SAME FILE? N_
NEW FILE? N_
The SPECTRUM FILE is the GC/MS data file
containing a peak or peaks to be quantified. The FIRST
SPECTRUM, SECOND SPECTRUM, and
SPECTRUM NUMBER OF MAXUMUM prompts
have the same meaning as described under QNTSET.
The STANDARDS FILE NAME is the peak area file
generated by QNTSET. The response to the PEAK
NUMBER prompt is the number of the entry in the
peak area file which is to be used to quantify the
unknown peak. For example, if the user has created a
peak area file containing three entries such as the
following, and wants to quantify a DDD peak, the
reply to PEAK NUMBER would be 2.
1. DDT
2. DDD
3. Malathion
50 nanograms
100 nanograms
80 nanograms
The program then prints the name of the compound
stored in the peak area file, and the computed number
of nanograms in the unknown. In the example 50
nanograms of DFTPP were taken and 54 nanograms
found using a 100 nanogram standard.
The SAME FILE prompt should be answered
positively if the user wishes to quantify another peak
from the same GC/MS data file. The NEW FILE
prompt should be answered positively if the user wishes
to quantify a peak from a different GC/MS data file.
MEASUREMENTS WITH QUAN3
This program works with data files acquired under
the control or IFSS modes or with the specialized SIM
programs CRTSIM and PLTSIM. The program is
104
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somewhat simpler to use than QNTSET and
QNTATE. Furthermore, it has the major advantage of
operating in the extracted ion current mode, i.e., if the
standards or unknowns were measured with the control
or IFSS mode using a range of mass units, QUAN3
may be used to quantify with a single mass range
shorter than the measured mass range, or a single mass
unit, or even a single fractional mass unit. The program
works by summing for all spectra between given limits
(inclusive) the abundances of all masses within the
given range (inclusive.) The baseline is subtracted
during the integration and the user may enter a
response factor which is a weighting factor for the
measurement. Sample dialogue for the program is as
follows:
SELECT MODE: QUAN3
STANDARD FILE NAME: REF100
SPECTRUM NUMBERS: 68-75
MASS RANGE: 442
SUBTRACT BASELINE: Y_
AMOUNT = 100
ABSOLUTE INTENSITY = + 124928.000
UNKNOWN FILE NAME: REF50
SPECTRUM NUMBERS: 68-75
MASS RANGE: 442
SUBTRACT BASELINE: Yj_
RESPONSE FACTOR: j_
ABSOLUTE INTENITY = + 67328.000
AMOUNT = + 53.893
UNKNOWN FILE NAME:
The data Hies used to illustrate this dialogue are the
same as those used to illustrate QNTSET/QNTATE
and MSSOUT. The STANDARD FILE NAME is the
data file generated by GC/MS of the standards, in this
case 100 nanograms of DFTPP. Quantitation was
accomplished using only molecular ion data although
the original data acquisition was over the 33-450 amu
mass range. Using a response factor of 1, the program
found 53.893 nanograms of DFTPP in the 50
nanogram injection. The unknown amount is given in
the same units as the standard amount.
MEASUREMENTS WITH MSSOUT
The integrate (IN) command of MSSOUT may be
used to integrate peak areas after the CM and EM
commands are issued according to the standard rules.
The CM and EM commands are described in section
4.2. The. IN command has the same advantage of
QUAN3 in that quantitation may be accomplished
using individual masses although abundance data from
the entire mass range was acquired originally.
However, MSSOUT has no apparent capability to
relate standard and unknown peak areas. Therefore
this final calculation, including the response factor,
must be accomplished by the user with a calculator or
some other manual procedure. Sample dialogue for the
IN option of MSSOUT using the same two DFTPP
data files is as follows:
SELECT MODE: MSSOUT
RUN NAME: REF100
DFTPP 100NG
CM
ENTER MASSES TO COLLECT. MAX =
47 442
"EM
ENTER MASSES TO PLOT
442
IN
START = 68
END = 7j5
. MASS SUM
442 126148
NA
RUN NAME: REF50
DFTPP SONG
CM
ENTER MASSES TO COLLECT. MAX =
47 442
EM
ENTER MASSES TO PLOT
442
IN
START = 68
END = 75
MASS SUM
442 68360
105
-------
As in plotting an EICP with MSSOUT, the specific
mass to be used in the IN command must be collected
with the CM command. The START and END
prompts produced by the IN command request the
starting and ending spectrum numbers of the peak. In
place of entering the spectrum numbers from the
keyboard, the user may touch the space bar which
displays the cross hair cursor. Moving the cursor to the
left and right sides of the peak, and pressing the space
bar after each, causes input of the spectrum numbers.
The NA command changes the name of the data file
from the standard file to the unknown file. Final
calculation using the formula described above gave
54.2 nanograms for the 50 nanogram injection.
Peak areas for more than one ion across a single peak
are obtained as shown below; in this case EM is
required to define the sequence of events for the IN
command.
EM
ENTER MASSES TO PLOT
198,442
'IN
START = 67
END =79
MASS SUM
198 100992
442 79752
6.3 OPEN TUBULAR COLUMN'S
The purpose of this section is to review the current
advantages, disadvantages, and applications of open
tubular columns in environmental monitoring with
GC/MS. It is clearly beyond the scope of this manual
to review in depth the entire field of open tubular
columns which is a very active area of current research.
The primary application for open tubular columns in
environmental monitoring is in the analysis of very
complex samples such as industrial and other waste
effluents. Another application is in the analysis of
samples that contain difficult to separate but
environmentally significant components such as both
pqjychlorinated biphenyls and chlorinated
berizodioxanes. However the user must recognize that
the use of high performance, high resolution open
tubular columns introduces trade-offs in analytical
operations:-Greatly improved resolution invariably
requires significantly more control of operational
variables. Therefore there is an important need to
understand the additional costs required to produce the
improved performance, and to apply the high
performance columns only in situations that truly
require them. For the majority of problems
conventional packed columns currently offer the best
combination of performance and operational conven-
ience. It is also of importance to realize that there is a
far greater need for high resolution performance with
conventional GC detectors than with a mass
spectrometric detector. With conventional detectors,
the retention index is the only output useful for
qualitative analyses. Therefore it is vital to acquire
accurate and precise retention data, and it is not
surprising to find that the leading proponents of open
tubular columns are users of conventional detectors.
With the mass spectrometric detector and the ability to
acquire several mass spectra across many GC peaks,
unresolved components may often be clearly
recognized, identified, and even quantitated using
characteristic ions from each component. Similarly
with selected ion monitoring high resolution often may
be of no real value. Nevetheless with complex mixtures
of compounds with complex spectra, open tubular
columns offer outstanding capabilities for GC/MS
application and may be the method of choice.
OPERATING VARIABLES
As previously indicated, it is not the intention of this
section to review comprehensively all possible
operational variables. However the ideas presented
seem to represent a consensus of the important
viewpoints of the most successful and experienced users
of open tubular columns.
By all means do not attempt to coat open tubular
columns unless you have a great deal of experience or
the time to acquire it. Commercial columns of high
quality are available from several sources, and the time
required to master and control the coating technique is
much greater than the cost of the commercially
available columns. Glass columns are strongly
recommended because they are chemically inert with
respect to most compounds.
Splitless injection is strongly recommended. The
method of stream splitting should be abandoned
because of significantly reduced sensitivity due to the
discarding of a large fraction of the injected sample,
and the uncertainty of reproducing the split ratio. A
particularly important variable with splitless injection
is the solvent. In general a solvent should be selected so
the initial column temperature may be set at least 20C
106
-------
below the boiling point of the solvent. This will permit
the operation of the so called solvent effect which acts
to concentrate the sample components into very
narrow bands giving maximum peak resolution. The
choice of solvent will usually be constrained by the
capabilities of the GC to achieve ambient or sub
ambient column oven temperatures. If the GC
equipment in use does not have low temperature
capability, the potential for achieving optimum peak
resolution with splitless injection and the most
desirable solvent will be sharply reduced. For example,
methylene chloride is strongly recommended in
chapter 3 for low boiling solvent extraction. Methylene
chloride is also an excellent solvent for use with open
tubular columns. However the solvent effect would
cause an undesirable peak broadening effect with
methylene chloride unless a satisfactory sub ambient
initial column temperature could be obtained. If sub
ambient temperature capability is not available, and
high performance is needed, a possible alternative is
replacement of the low boiling solvent with a higher
boiling one. This of course may not be practical because
of solubility or other considerations, adds to the
complexity of the procedure, and the higher boiling
solvent could contribute undesirable background to the
sample.
Two of the most critical factors which operate to
reduce column lifetime to unacceptable levels are
repeated violations of the high .temperature limit of the
column, and the injection of samples containing water.
These conditions should be avoided. With splitless
injection samples of the order of 1-2 microliters may be
injected into the system. Columns prepared by
commercial suppliers using the newer methods of
manufacture can withstand routine direct injections of
several microliters of pentane, hexane, methylene
chloride, or carbon disulfide for months without
damage. Some solvents, such as methanol, are not
recommended, but the manufacturer's instructions
should be carefully noted when choosing solvents.
The application of open tubular columns has several
implications for all data systems. Very sharp GC peaks
require scan speeds that are relatively fast, and if all
mass spectra are saved on a computerized storage
device, sufficient space must be available to store the
potentially large number of spectra generated during a
long elution period. The PDP-8 data system has several
features that facilitate the use of open tubular columns,
but reasonable caution is required for this and any
other data system that was not specifically designed for
this application.
In section 2.7 under FAST SCAN OPTION and the
following paragraphs, the basic sweep speed
considerations of the PDP-8 data system are explained.
Insertion of the fast scan option hardware causes the
settling time for each mass set voltage to be reduced
from 2.3 msec to 1 msec, with some improvement in
scan speed. Another method of improving sweep
speeds is to apply the IFSS method of data acquistion.
The following dialogue shows operating parameters
that give a 2.5 sec sweep with a 2.3 msec settling time.
Use of a 1 msec base integration time reduces the sweep
time to about 2 sec.
SELECT MODE: IFSS
CALIBRATE?: N_
TITLE: OPEN TUBULAR TEST
CALIBRATION FILE NAME: CAL
FILE NAME: SAMPLE
MASS RANGE: 33-450
SAMPLES/AMU: J_
MAX RPT COUNT: 5_
BASE INTEGRATION TIME: 2_
RPT COUNT BEFORE CHECKING
LOWER THRESHOLD: 2_
LOWER THRESHOLD: 3_
UPPER THRESHOLD: J_
RT ON CRT?: N_
RT GC ATTEN: 5_
MS RANGE SETTING?: H_
MAX RUN TIME: 30
DELAY BETWEEN SCANS (SECS.)?
DATA
Software exists to cause a data file to begin on the
first disk drive (unit 0) of a two disk system, and
conclude on the second disk drive (unit 1) if insufficient
space is available on unit 0. The files required are
TWIN and EXMOD2, and bit 11 of the hardware
status word at location 2060 in INITSS must be a one
(see section 7.1).
6.4 CHEMICAL lONIZATION(CI)
The purpose of this section is to review the current
advantages, disadvantages, and applications of
chemical ionization (CI) in environmental monitoring.
It is not a purpose to review the entire field of CI, which
is very broad in scope and a very active area for current
research. . -*
The primary application of chemical ionization in
environmental monitoring is to obtain the additional
107
-------
information necessary to accurately identify
compounds that are not reliably identified through
their electron ionization (El) spectra. Most often
additional information will be required in situations
where a molecular ion is not observed in the El
spectrum, and where ail' authentic standard is not
available for acquisition of other supporting
information such as a GC retention time. The problem
of quality assurance in compound identification is
discussed further in section 5.3.
Another" important application of CI is in selected
ion monitoring where ions formed in CI processes are
sometimes more selective and abundant than ions in
the El spectrum of the same compound. An advantage
of CI is that significant diagnostic fragment ions are
sometimes present that, are not observed in the El ;
spectrum. This advantage would be of value to those
engaged in the interpretation of spectra of unknown
compounds whose El spectra do not appear in mass
spectral libraries. A potential future application is
negative ion CI. Negative ions have been shown to be
generated by some compounds in much greater
abundance under CI conditions than under El
conditions. However, most current instruments cannot
observe negative ions without major modifications, and
the significance of this technique is not yet fully
demonstrated.
At the present time most types of chemical
ionization cannot stand alone as the primary method of
ionization in broad spectrum organic analyses as
defined in this manual. There are several reasons for
this situation. First many .compounds give, with the
popular reagent gases, CI spectra consisting mainly of
molecular ions and molecular ions containing a proton
or some hydrocarbon fragment. Therefore these
spectra are less useful for identifications than the
corresponding El spectra which often contain many
structurally significant fragment ions. Secondly,
although many compounds show fragmentation in
their CI spectra, CI spectral libraries have not yet been
developed. Therefore, interpretations of spectra are
required, and this is a relatively slow process compared
to empirical spectrum matching.
In addition to the problem of the sometimes
confusing M + 29, M+41, and other extraneous ions in
some types of CI spectra, there are problems associated
with the large number of operational variables of CI.
These variables sometimes lead to significantly
different CI spectra "produced from the same
compound by different laboratories and instruments.
This makes interlaboratory comparisons difficult and
discourages spectral library^ development. The
principal variables appear to be reagent gas, ion source
design, ion source temperature, and ion source
pressure. Other variables^ such as certain ion source
potentials, electron energy, etc. may also be important.
One approach to generating comparable spectra from
different instruments in different laboratories is the use
of a standard reference compound to calibrate the
experimental variables. Of course this should be used in
connection with temperature and. pressure gauges and
other operating parameter controls. Unfortunately
some equipment sold commercially does not include
essential controls. Also temperature, pressure, etc.
gauges are not always reliable indicators because these
devices depend on. transducers that are subject to
variable-output after aging or contamination.
METHANE CHEMICAL IONIZATION
REFERENCE COMPOUND
The El GC/MS reference compound decafluorotri-
phenylphosphine (DFTPP) is particularly well suited
as a methane CI reference compound. The methane CI
spectrum of DFTPP displays, in addition to an
abundant M+l ion at mass 443, several major
fragment ions that are of very low abundance in the El
spectrum. Therefore the CI spectrum is an excellent
indicator of the presence of correct CI conditions.
Figure 6.5 shows the dependence of the fragmentation
pattern of DFTPP (methane CI) on the ion source
temperature. At temperatures below 150C the ions at
masses 423 (loss of F) and 365 (loss of a phenyl group)
are the most abundant in the spectrum. In the
corresponding El spectrum both of these ions are below
5% relative abundance. As the temperature of the ion
source in the CI experiment was increased, thermally
induced fragmentation increases until, at temperatures
above 200C, the base peak is mass 169 and very little
M + l ion was observed. The methane CI spectrum of
DFTPP at an ion source temperature of 90C as
displayed in Figure 6.5 is proposed as a reference
spectrum for methane CI measurements.
The methane CI of DFTPP is much less sensitive to
ion source pressure in the range commonly used for CI
measurements. However overall sensitivity is a
significant function of ion source pressure.
PRINCIPLES OF CHEMICAL
IONIZATION
In chemical ionization electrons are used to ionize a
reagent gas which subsequently ionizes sample
molecules by chemical reactions, i.e. proton transfer,
hydride abstraction, ion attachment, etc. Chemical
108
-------
Ion source 90C
-w--'-
ioc
Ion source 150C
L JL
IOC 150
Ion source l80C
iOC
.r>c
,L ,.,, Ul ...1 , ...
id ,lj
,,,,.]
.|.,H.iti.
J,,
1 I- M L '
4'jc
Ion source 23
... L 1
100 150 20
2£0 -ICC 3^0
Figure 6.5 Chemical ionization (methane) mass spectra of DFTPP as a function of ion source temperature on the
Finnigan model 4000 GC/MS System.
109
-------
ionization is usually a much less energetic process than
electron ionization. Electron ionization generates
molecular ions with an internal energy of 500 to 1000
kcal/mole, and in order to release such energy, these
ions may^undergo rearrangements and fragmentations.
Often the most important piece of information in a
mass spectrum, the mass of the molecular ion, is lost,
and only'fragment ions will be apparent. In contrast,
initial ions formed by a chemical ionization process
usually have an internal energy of only 50 to 100
kcal/mole, which means that CI spectra usually exhibit
intense ions in the molecular weight region. Chemical
ionization has been shown to offer sensitivity at least as
good as electron ionization, and offers the advantage of
allowing -.characterization of the sample's chemical
reactivity through the choice of reagent gases. While
methane has been the most widely used reagent gas, a
number of others, singly and in combination, have been
successfully used to produce CI mass spectra. Popular
reagent gases include hydrogen, helium, argon-water,
ammonia, and nitric oxide.
When methane is bombarded with high energy
electrons, primary reaction 1 takes place.
Figure 6.6 shows a comparison of the El and CI mass
spectra of octadecane. The El spectrum shows a base
peak at mass 57. The CI spectrum shows the
characteristic ion at mass 253 (M-l) formed according
to equations 7 and 11.
There are usually two options for handling the
carrier gas in CI. The carrier gas may be used as the
chemical ionization reagent gas, and no enrichment
device is required. This has the advantage of improved
sensitivity since all of the chromatographic effluent
enters the spectrometer. It has the disadvantage of
requiring the use of unusual carrier gases and perhaps
changing chromatographic behavior. Alternatively the
usual GC carrier gases may be used with an enrichment
device, and then the CI reagent gas introduced into the
GC inlet line just prior to the effluent entering the ion
source. With this method some sample will be lost, but
the customary GC carrier gases may be retained with
the considerable flexibility of adding a variety of
reagent gases. The latter approach is necessary with
open tubular columns since the low flow rates used are
inadequate to give appropriate reagent gas ion source
pressures. A modern, well designed chemical ionization
CH4
CH,+
CH:"
CH' + H/
If the gas is present in a confined chamber at a pressure
of approximately one mm of Hg, i.e. if it is in a CI mass
spectrometer source, the following secondary reactions
can take place (2 through 5):
IT
2e
(i)
CH4+
CH4 -^
CH,* + CH4
CH,+ + CH, -
C5H3+ + CH<
CH3
H2
Hr
(2)
(3)
(4)
(5)
In a normal CI source, at a pressure of one mm, CH,*
and CH;+ will comprise about 90% of the total
ionization, while CjH^ will be about 5%. If a sample
molecule, MH, is present at a pressure much less than
the reagent gas, it can react with the above ions in the
following manner (Reactions 6 through 11):
mass spectrometer should be equip'ped for all of the
above options, and a system for rapid switching among
them.
6.5 ACCURATE MASS
MEASUREMENTS
The purpose of this section is to briefly review the
concept of accurate mass measurements and their
application to compound identification. As with
several other sections in this chapter, a comprehensive
review of the subject is beyond the scope of this manual,
and the user is directed for more information to several
excellent books referenced in the Bibliography.
Although only a small fraction of the mass
spectrometers manufactured have accurate mass
measuring capability, it is important that the user of a
conventional GC/MS system recognize the existence of
CHJ + MH CH4 + (MH:)* (proton transfer) (6)
CHS+ + MH -^CH< + H, + (M)T (hydride abstraction) (?)
C2Hr + MH -» (MH + C2H,r (ion capture) (8)
110
-------
C2H,+ + MH -~ C2H4 + (MH,)* (proton transfer) (9)
CjH," + MH »(MH + CjH,)* (ion capture) (10)
C,H5* + MH »CjH6 + (M)+ (hydride abstraction) (ii)
this capability. For certain samples of particular
significance the most important decision may be to
make arrangements for an accurate mass measurement
of one or more ions.
Accurate mass measurements are defined as
measurements made to 0.01 amu or better and are
important because this degree of accuracy may allow
an accurate determination of the atomic composition
of the ion. This information is a powerful aid to the
identification of unknowns, particularly in situations
where a matching or similar spectrum is not
available in a mass spectral library. For example,
both acetone and njsutane exhibit a molecular ion at
mass 58. However, because of the mass defect of the
constituent atoms of each ion, i.e., the deviation of
the actual atomic mass from the nominal integer
number, the acetone ion has an accurate mass of
58.0417 while the isobutane ion has a mass of
58.0780. Therefore, these two ions differ in mass by
36.3 millimass units (mmu). Both have a positive
mass defect, that is, their mass defects are in excess of
the nominal integer value. Mass defects can also be
negative, in which case the accurate mass is less than
the integer mass number. In order to distinguish
between these two adjacent mass spectral peaks, they
must be separated or resolved. One common
definition of resolution states that two peaks are
resolved when the valley between them is ten percent
of the overall peak height. Resolution is
mathematically defined as M/deltaM, where M is
the nominal mass of the two ions to be separated, and
deltaM is the difference between them. Using the
example of mass 58 ions of acetone and njsutane, a
resolution of 1600 would be needed to resolve them.
The calculation is shown below.
Resolution =
M
delta M
58
.0363
= 1600
This is considered moderate resolution. Resolution
in excess of 8000 is considered high since that amount is
usually necessary to resolve most mass doublets. In
order to achieve such resolution, double focusing of the
ion beam is usually necessary. A magnet focuses only
on the basis of mass, but an electrostatic analyzer, i.e. a
set of curved plates with a voltage impressed on them,
will focus ions on the basis of their kinetic energy.
Adding such extra focusing reduces the overall
quantity of ions traversing the mass spectrometer, and
thus reduces overall sensitivity. To overcome such a
reduction, the mass range is usually scanned at a slow
rate. To minimize the effects from slow scanning and
decreased sensitivity, one should only use as much
resolution as necessary .to perform the required
analysis, always keeping in mind that the accuracy of a
mass measurement is independent of resolution as long
as any mass doublets are separated.
Accurate masses of ions can be determined by
several methods, but the two most common are peak
matching and computer acquisition. Peak matching
involves a comparison of the unknown mass spectral
peak wih a known ion peak, usually from a standard
material such as perfluorokerosene (PFK). By
switching the accelerating voltage rapidly such that the
unknown and known ions are alternately focused on
the collector, one can overlay or match the two ions,
measure the ratio of their masses, and therefore
determine the mass of the unknown ion. The computer
acquisition method of determining accurate masses
depends upon a computer finding two relatively close
reference masses, and then interpolating between them
to identify the exact mass of an unknown ion.
Once the mass of an ion has been accurately
measured, it is a relatively easy matter to determine
what combination of atoms will add up to that number.
Several tables have been published which list accurate
masses and the corresponding composition formulas.
However the most effective approach is to use a
computer program to find all possible compositions
whose masses are within the probable error of the
accurately measured mass. Listed below is an
interactive program written in the Basic language that
finds all possible carbon, hydrogen, nitrogen, and
oxygen compositions that fall within the range of a
measured mass plus or minus the probable error. The
program is constrained further by a user imposed
limitation on the number of oxygens or nitrogens it
may use in any given formula. This constraint was
inserted to rule out a large number of formulas
containing unreasonable numbers- of these-elements. It
111
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E
8.
8.
OCTfPEDTC El
219 3D « SO GO 70 88 SO 108 U8 128 130 J« 1SB 160 170 188 ISO 8BB 218 220 230 Vffi 2SB
MX E
B
8_
8.
N-OCTHECFIC Cl
5R-
TO BO so ice iie 120 130 i« iso ira ITS in ise aao 210 220 230 z«
E
2SB Z9B 273 2B9 29 369
Figure 6.6 Comparison of the El and C! mass spectra of Octadecane.
112
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is usually possible to guess at the maximum number of
oxygens and nitrogens, run the program, and if too few
or too many formulas are found, change the guess and
run it again. Also no formulas will be found which
contain an extremely small number of hydrogens
relative to the number of carbons. Atoms other than N
or O could be included in the program by modifying it,
or by substituting their masses for N or O in the
program.
0002 PRINT "WHAT IS YOUR PRECISE MASS,
INTEGER AND DECIMAL PARTS?"
0004 INPUT M
0006 PRINT "WHAT IS YOUR ERROR, E.G.,
.002,?"
0008 INPUT E
0010 PRINT "WHAT IS THE MAXIMUM
NUMBER OF OXYGENS TO BE
CONSIDERED?"
0012 INPUT O
0014 PRINT "WHAT IS THE MAXIMUM
NUMBER OF NITROGENS TO BE
CONSIDERED?"
0016 INPUT N
0018 LET A=M/12
0020 LET A=INT (A)
0022 LET L=INT (M)
0024 FOR J=0'TO 0
0026 FOR K=0 TO N
0028 LET C = A
0030 LET B=L-C*12-J*16-K»14
0032 IF B
-------
CHAPTER 7
AUXILIARY
A number of computer programs are used directly in
the acquisition and output of data from the
computerized GC/MS system. The use of these
programs is described, with specific examples, in the
chapters on GC/MS operations and Quality Assurance
(Chapter 2), Data Output (Chapter 4), Compound
Identification (Chapter 5), and Advanced Analytical
Techniques (Chapter 6). There is another group of
computer programs which are used to evaluate the
performance of certain hardware components of the
data acquisition and control system. The use of these
programs is described, with specific examples, in the
chapter on Preventive Maintenance (Chapter 8) and
Trouble Shooting (Chapter 9). Finally there is a
miscellaneous group of computer programs that are
useful in working with the GC/MS system, but do not
fit into any of the above categories. The purpose of this
chapter is to describe the application of these with
specific examples. Some of these programs operate
under the GC/MS real time operating system, and
some of them are best used only with an auxiliary
operating system. The choice of an auxiliary operating
system is of some importance as several systems are
available.
The OS-8 operating system requires 8K of core
memory and has the advantage of being supported and
maintained by the Digital Equipment Corporation. It is
very widely used by thousands of installations across
the country, and a great deal of utility software is
available for use with it. However, it would be
impossible to switch all the mass spectrometer
programs over to OS-8 because it is not a real time
operating system.
The X-System is an older utility system that requires
only 4K of core memory. It was developed at Stanford
University and System Industries acquired it from the
Digital Equipment Corporation Users Society
(DECUS). As far as is known it is not supported or
maintained by anyone, a large number of bugs exist in
some of the programs on some versions, and the kind of
software usable with it is extremely limited.
For the reasons given above the OS-8 system is
strongly recommended as the standard PDP-8
auxiliary operating system. The X-system will not be
discussed in this manual, and any user who wishes
information about it may acquire limited
documentation from DECUS (DECUS No. 8-64a) or
System Industries.
7.1 REAL TIME OPERATING SYSTEM
All the programs discussed in this section are found
on the standard system disk and are used under that
operating system. Additional programs may be loaded
onto and run from the real time operating-system.
Instructions for loading these are given in section 7.2.
TAPE INITIALIZATION PROGRAMS
These programs are required to initialize a formatted
Dectape or industry standard 9 track magnetic tape for
use with programs or data files. The program
NEWTAP is used to initialize Dectapes with either
type controller (see section 9.2):
SELECT MODE: NEWTAP
MOUNT NEW DECTAPE ON UNIT 1
(TC08 controller)
MOUNT NEW DECTAPE ON UNIT 0
(TD8E controller)
SELECT MODE: LIST
TAPE?: Y_
NAME BLOCK
ENTRIES LEFT =174
BLOCKS LEFT = 5525
NEXT AVAILABLE BLOCK =
15
114
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If you have available an industry standard 9-track
magnetic tape with the Datum controller, the
corresponding program is NEWMAG. The Dectape
unit must be write enabled and an industry standard
magnetic tape must have a write ring inserted.
FILE COPY, DUPLICATION, AND
SAVE PROGRAMS
Program and data files may be copied from one
storage device to another (Dectape, disk, or industry
standard magnetic tape) with the COPY program.
Sample dialogue for disk to disk transfer is as follows:
SELECT MODE: COPY
FILE NAME: FILE TO BE COPIED
RENAME? FILE MAY BE RENAMED
FROM DISK? Y_
UNIT NO.: 0_
ONTO DISK? Y_
UNIT NO.: 1
If a transfer to or from Dectape is desired, a Njesponse
is made to the FROM DISK? prompt or the ONTO
DISK? prompt. This causes the program to enter the
Dectape dialogue. The user must be aware that there
are two different programs named COPY. One version
copies files among disk units 0-3 and TC08 Dectape
units 0-7. The other version copies files among disk
units 0-3 and TD8E Dectape unit 0, and calls the
program MAGCPY which copies files to and from 9
track industry standard magnetic tape. If a transfer to
or from industry standard magnetic tape is desired, a M
response is made to these prompts. The industry
standard magnetic tape must be unit 0. To copy files to
an industry standard magnetic tape, a write enable ring
must be installed on the tape reel. This function is
accomplished with a Dectape by pressing the write
enable switch.
A system disk or Dectape may be duplicated (copied
in its entirety) with the program CPYDSK if two disk
drives or two Dectape drives are present, which implies
a TC08 Dectape. The dialogue for this program is as
follows:
SELECT MODE: CPYDSK
FROM DISK? Y_
UNIT NO.: 0_ ~
ONTO DISK? Y_
UNIT NO.: 1
SELECT MODE: CPYDSK
FROM DISK? N_
TAPE UNIT NO.: _1_
ONTO DISK? N^
ONTO TAPE UNIT NO.: 0_
Industry standard magnetic tape to industry standard
magnetic tape duplications are not supported.
A very versatile and useful program called SAVE is
available to transfer parts of data files from one system
disk or Dectape to another, or to segment data files on a
single disk. The original intent of this program appears
to have been to give the operator the capability of
saving a collection of mass spectra of various
compounds using different spectra selected from
different data files. However, the program SAVE has
broader applicability and may be used to reduce the
size of data files by saving, under a new file name,
contiguous groups of spectra that correspond to the
parts of a chromatogram that contain the peaks. The
original data file is then deleted and many useless
spectra of leading, interspersed, or trailing baseline are
purged from the storage device. It is very important to
recognize that the SAVE program does not maintain
the original spectrum index numbers, but renumbers
the spectra in the saved file. Therefore all sense of
retention time is lost, and if this information is desired,
a TICP of the original data file should be plotted before
executing the SAVE program. In the sample dialogue
shown below, the SAVE program is used to segment a
data file containing 372 spectra but contains all the
relevant information except retention time. All of the
conventional output programs described in chapter 4
may be used with the reduced and saved data file to plot
TICP's, EICP's and mass spectra.
SELECT MODE: SAVE
FILE NAME: RW147B
RENAME: Y_
NEW FILE NAME: SRW147
FROM DISK? Y_
UNIT NO.: J_
ONTO DISK? Y_
UNIT NO.: 0_
SPECTRUM NUMBERS:
170-200;230-290;300
In this example the original data file was on disk unit
1 and the new data file is saved on disk unit 0. It is not
necessary to transfer a file to another unit with the
SAVE program. If the original and saved data files
have different names, they may be located on the same
115
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device. A negative response to the ONTO DISK?
prompt causes the program to enter the Dectape
dialogue, and the new 'data file may be saved on
Dectape. The SAVE program does not support an
industry standard magnetic tape. The user should be
aware that there'are two version of SAVE; one handles
TC08 Dectapes 0-7 and disks 0-3; the other handles
TD8E unit 0 only and disks 0-3.
In the same dialogue a single spectrum No. 300, was
saved illustrating this capability. It should be noted
that there is no background subtract capability in the
SAVE program and it is the background subtracted
spectrum that should be saved in any collection of
individual mass spectra. Therefore the feature of the
plotter output routine (Chapter 4) that allows the
operator to save a subtracted file should be used first
and the background subtracted spectrum saved with
the SAVE program.
FILE DELETE AND SYSTEM
TAPE DUMP PROGRAMS
The program DELE is a housekeeping program
which removes programs or data files from the disk or
Dectape directory. It is essential for a GC/MS operator
to maintain an orderly storage system and 'delete all
unneeded files. The dialogue for the program is:
SELECT MODE: DELE
FILE NAME: FILE TO BE DELETED
TAPE?: Y_(if the file is on tape)
N_ (if the file is on disk)
This program operates most efficiently if files at the end
of the list are deleted first, followed by older files. The
user should be aware that there are two versions of
DELE; one handles TC08 Dectape unit 1 and disk 0;
the other handles TD8E unit 0 and disk 0.
An alternative program, BCDELE, is more efficient
in deleting files, but requires the presence of an
extended arithmetic element (EAE) and 8K core in the
PDP-8. More information on the EAE is included in
section 4.2 on the MSSOUT software. BCDELE will
remove from disk unit 0 only contiguous groups of files
as in the following example:
MOUTP4 7431
SAMP1 7457
SAMP2 7465
SAMPS 7473
SAMP4 7501
SAMP5 7507
SAMP6 7515
SAMP7 7'523
SAMPS 7531
SAMP9 7537
SAMP10 7545
SELECT MODE: BCDELE
SAMP1:SAMP2
"SAMP5:SAMP6
"SAMP8:SAMP9
" press return
MOUTP4 7431
SAMPS 7457
SAMP4 7465
SAMP7 7473
SAMP10 7501
System dump programs cause the entire contents of
the system disk to be copied to Dectape or industry
standard magnetic tape in a form that is suitable for
their recopying by another program onto a formatted,
but otherwise empty disk cartridge. The value of this
program is in creating a number of new disk cartridges
containing identical system software from a single
dump tape. Sample dialogue for the SYSDMP
program, which dumps the system to Dectape, is:
SELECT MODE: SYSDMP
7 TAPES WILL BE NEEDED
MOUNT REEL 1 ON UNIT 1
The corresponding program for industry standard
magnetic tape is called MAGDMP. The method of
restoring dump tapes to system cartridges is discussed
under the OS-8 operating system. Again the user
should be aware that there are two versions of
SYSDMP, one for TC08 Dectape units 0-7 and one for
the TD8E Dectape unit 0.
PROGRAM TO CHANGE MACHINE
LANGUAGE INSTRUCTIONS
The program PATCH is an extremely dangerous one
because it allows the user to change machine language
instructions in programs as they are stored in disk files.
The program is important because certain changes are
sometimes essential. An example is the change of status
bit 10 in location 2060 of INITSS to permit use of
Ml000 to calibrate with tris(perfluoroheptyl)triazine.
The procedure for this change is as follows:
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SELECT MODE:
FILE: INITSS
(computer halts)
PATCH
Examine location 2060 and modify to assure that bit
10=1; for example, load address 2060, examine
contents (this process bumps the address to 2061); load
address 2060, set all switch registers to 0 or 1, press
deposit key; set switch register to 0200, press load
address, clear, and continue. The system will boot.
Bits in location 2060 have the following significance:
bit 0=no l=yes
0 Second TC08 Dectape for data acquisition
1 TC08 Dectape system
2 Dual drive TC08 Dectape
3 Disk system
4 Dual disk system
5 IFSS interface
6 Plotter
7 TD8E Dectape or 9 track tape or cassette
8 CRT
9 Disk monitor in core
10 1000 amu file handling
11 One millisecond timing board
(fast scan option)
PROGRAM TO START THE
OS-8 SYSTEM
The OS-8 system may be started by inserting an OS-8
disk cartridge, and then entering into the switch
register a bootstrap loader. An alternative method is to
start a system program, then insert an OS-8 disk
cartridge. The system program is called OSDGO and
sample dialogue is as follows:
SELECT MODE: OSDGO
PLACE OS/8 CARTRIDGE IN DRIVE;
WAIT TIL READY; THEN
PRESS CONTINUE
7.2 THE OS-8 OPERATING SYSTEM
If a real time system disk is not up and running, it is
simpler and quicker to start OS-8 by entering tfie OS-8
bootstrap program into the switch register and running
it in the usual manner. See section 2.3 for instructions
on loading a program into the switch register. If a
system disk is up and running, it is simpler to start OS-8
with the program described in the previous section. The
OS-8 bootstrap is as follows:
Address Instruction
0000
0001
0002
0003
0004
0005
6502
0000
6517
6512
6514
5005
If this program runs successfully, a period will be
printed on the console output terminal. If the program
fails to run properly the first time, it must be reloaded
and restarted. This short bootstrap is of the type that is
destroyed as the OS-8 system loads, but a new
bootstrap is created at address 7600. Therefore after a
successful start if it is necessary to halt the computer,
OS-8 may be restarted at address 7600.
An extensive discussion of the OS-8 operating system
and many of the programs found on the OS-8 system is
well beyond the scope of this chapter or this manual.
Users who desire additional information should consult
the OS-8 handbook (Digital Equipment Corporation
part number DEC-S8-OSHBA-A-D, about $5.00). The
only programs discussed in this chapter are those
relevant to GC/MS system operations and
maintenance.
TAPE FORMAT PROGRAMS
Dectape must be formatted using a program
analogous to the disk cartridge format program. Two
programs are available named DTFRMT and
TDFRMT and these apply to Dectapes using the TC08
and TD8E controllers respectively. Mount the Dectape
to be formatted on the drive and select a unit number
with the thumbwheel switch. Turn each tape twelve
turns onto the take-up reel, place the WRITE
LOCK/WRITE ENABLE switch in the write enable
position, and the LOCAL/REMOTE switch in the
remote position. The NORMAL/WRTM switch is on
the front of the TC08 tape controller behind the facing
panel and this must be placed in the WRTM position.
With the TD8E controller the corresponding switch is
located on the upper right corner of the M868 board on
the PDP-8 bus. It is necessary to slide the PDP-8
forward and remove the lid to see the switch. Its
normal position is off and the format position is labeled
WTM. Call the format programs under OS-8 as
follows:
117
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.R DTFRMT (TC08 controller)
DTA? j_
DIRECT? MARK
0201 WORDS, 2702 BLOCKS. OK?
(YES OR NO)
YES
SET SWITCH TO NORMAL
.R TDFRMT (TD8E controller)
2702 BLOCKS. OK?
UNIT? 0_
FORMAT? MARK
0201 WORDS,
(YES OR NO)
YES'
SET SWITCH TO WTM
(after one pass down the tape)
SET SWITCH TO NORMAL
The response to the first prompt is the Dectape unit
number selected. On a dual drive system two unit
numbers may be entered to format two dectapes. After
one pass of the tape the message SET SWITCH TO
NORMAL is printed. Set the switch to NORMAL (or
OFF) and press the return. At the conclusion of the
formatting, the program returns to the second prompt
and additional Dectapes may be formatted. After all
the Dectapes are formatted, halt the program and
restart OSS at address 7600.
PROGRAM TO LIST FILES ON THE
OS-8 SYSTEM
There are several methods of listing the names of the
files on the OS-8 system. These are described in detail
in the OS-8 handbook, and only one method is
described briefly in this section. One point to remember
is that the OS-8 system disk is divided into two parts, a
system area and a default storage area. Files in both
areas may be listed with the program PIP as follows.
.R PIP
SYS:/E
'/E
Entry of the command /E without designating the
SYS: area causes the program to list the files in the
default storage area.
PROGRAMS TO BUILD REAL TIME
SYSTEMS FROM TAPE DUMPS
A real time system tape dump contains all the files
necessary to regenerate a new disk. These dumps are
prepared using the programs SYSDMP or MAGDMP
as described in section 7.1. A single dump tape may be
used to generate a number of system disks. Three
programs are available which are named TC8RES
(TC08 Dectape controller), TD8RES (TD8E Dectape
controller), and MAGRES industry standard magnetic
tape).
The two Dectape programs operate very much the
same. In each case the first reel of the dump tape (there
may be one or more reels depending on the number of
data files included in the dump) should be mounted
before calling the program. If a TC08 Dectape
controller is present, mount the tape on unit 1; if a
TD8E controller is present, select unit 0. The Dectape
drive should be in the write lock position to protect the
dump tape in case of an error. The sample dialogue is as
follows:
.R TC8RES
.R TD8RES
(TC08 controller)
(TD8E controller)
MOUNT REEL 1 ON UNIT 1
(TC08 controller)
MOUNT REEL 1 ON UNIT 0
(TD8E controller)
At this point remove the OS-8 cartridge and install a
formatted disk cartridge. This cartridge may contain
files and programs, but they will all be replaced by the
real time system files. Press the return when the disk is
up to speed. After the restoration is complete, the
operator may start the new system by responding Y_to
the START SYSTEM prompt. A negative response
causes the computer to halt. Another cartridge may be
restored without reinserting the OS-8 system. Place
another formatted cartridge in the drive and restart the
restore program at address 0200.
The MAGRES program is used very much the same.
The write ring should be removed from the dump tape
and the disk controller format switch on the rear of the
disk controller should be placed in the format position.
LOADING NEW PROGRAMS ON OS-8 OR
THE REAL TIME SYSTEM
Programs may be transferred from the OS-8 system
to the real time system and run under this system.
Similarly programs may be loaded onto the OS-8
118
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system from OS-8 Dectapes or paper tape. Finally new
programs may be written in PDP-8 assembly language
with the use of the OS-8 operating system, and
transferred as above. All of these transfers are possible
using a variety of OS-8 options, and is well beyond the
scope of this manual to describe all of the possibilities.
The user should consult the OS-8 handbook for
detailed documentation. This section does present
instructions for a few simple transfers that are
especially valuable.
Inserting a Paper Tape Handler in OS-8. Some OS-8
system disks are not set up to handle paper tape input
from a teletypewriter. This insertion is required just
once and is accomplished by entering the following
commands to the OS-8 monitor:
.RUN SYS BUILD
$ INSERT KS33,PTR
$ BOOT
SYS BUILT
.SAVE SYS BUILD
Loading a Paper Tape File on OS-8. Paper tape files
come in two basic varieties: binary and ASCII formats.
Binary tapes are usually labeled FILENAME.BN and
ASCII tapes are labeled FILENAME.PA. One may
load a program from a binary file onto the OS-8 system
and run it.with the OS-8 R_ command by using the
following procedure:
.R ABSLDR
PTR:
(insert paper tape into the reader in the
region where only the parity bit is punched;
start the reader)
The program will print an asterisk after reading the
tape. Stop the paper tape reader and enter a control/C.
After the period is printed, enter the following
command:
.SAVE SYS: FILENAME
Either ASCII or binary paper tape files may be
transferred to the OS-8 system area with the program
PIP. If the file is in ASCII format, use the /A option; if
binary use the /B option.
.R PIP
SYS: FILENAME.PA < PTR:/A
(insert paper tape into the reader
In the region where only the parity
bit is punched; start the reader)
The program will print an asterisk after reading the
tape. Stop the paper tape reader and enter a Control/C.
Loading a Dectape File on OS-8. An OS-8 Dectape
file may be transferred to the OS-8 disk by several
programs. The program FOTP is convenient since it
automatically generates the same filename on the disk
as was present on the Dectape, and several files may be
transferred with one command:
.R FOTP
SYS: < DTA1:Filename.BN
This command would cause a binary file on Dectape
unit 1 to be transferred to the OS-8 disk. Under the OS-
8 system Dectape units 0 and 1 are usually reserved for
TD8E controllers and Dectape units 2 and 3 are
usually reserved for TC08 controllers. More
information on this program is found in the OS-8
handbook.
LOADING A BINARY PROGRAM ON
THE REAL TIME SYSTEM DISK
A binary file program on the OS-8 system may be
transferred to the real time system disk with the
following procedure:
.R ABSLDR
SYS: FILENAME, LOD150/G
This causes the file to be loaded on the real time system
to be placed in core memory; a second binary file called
LOD150 is also loaded and started by the /G option.
LOD150 is a program that has several other versions
named DLOADO and LOADIT. LOD150 produces
the dialogue:
FILENAME
FILE NAME:
P.A.: enter page addresses
P.A.: e.g., 0200-7577
P. A.:
(1 if Dectape)
0020-0157
ONTO UNIT NO.: 0_
ONTO TAPE?: N
(Y if Dectape)
Before pressing the return remove the OS-8 disk and
insert the real time system, disk. Press return when
ready and the message FILE HAS BEEN LOADED
wilfbe printed at the completion of the transfer.
119
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PROGRAM TO DUPLICATE OS-8
The 'program CPYDSK, described in 7.1, will
duplicate the OS-8 system. On OS-8 disks it is listed as
DSKCPY, but the dialogue is the same.
PROGRAM TO START THE
REAL 'TIME SYSTEM
The OS-8 program MSDGO will start a GC/MS
system disk as follows:
.R MSDGO
PUT S/150 CARTRIDGE IN D'RIVE;
WAIT TIL READY; THEN
PRESS CONTINUE
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PREVENTIVE MAINTENANCE
The purpose of this chapter is to gather together in
one place preventive maintenance information for the
complete computerized GC/MS system. As in several
other chapters, some detailed information is
specifically oriented to the Finnigan quadrupole mass
spectrometer with a data system that uses a Digital
Equipment Corporation model PDP-8 computer.
However a significant amount of information is of a
general nature and is- applicable to any computerized
GC/MS system. The sections in this chapter do not
repeat detailed instructions that are adequately covered
in manufacturers' manuals. The user is referred to these
instructions in the appropriate manual.
Preventive maintenance is perhaps more important
with a mass spectrometer than any other instrument
system. This is because the mass spectrometer vacuum
system is turned on 24 hours per day, 7 days per week.
The failure of a relatively simple component at an
inappropriate time can result in the total destruction of
an expensive and vital part of the system and therefore
make the total system useless.
8.1 MASS SPECTROMETER
VACUUM SYSTEM
MECHANICAL PUMPS
The oil in mechanical pumps must be changed
occasionally. The frequency of oil changes is
determined by the number of samples introduced that
contain high concentrations of materials. Heavy use of
a direct inlet system invariably leads to rapid
contamination of the pump oil. In general for a heavily
used system, the mechanical pump oil should be
changed at least once a year. If the system is used
mainly for GC/MS work with relatively clean samples,
a longer period may be acceptable. Similarly, heavy use
of a direct inlet system may require an oil change every
six months. The direct drive pumps may require
attention every six months regardless of the sample
load. Edwards No. 16 oil and Welch DUO-SEAL oil
are acceptable as pump oils. Direct drive mechanical
vacuum pump fluid should be used in the Alcatel
pumps.
Mechanical pump oils should be purged occasionally
for a few seconds to vent impurities. This is
accomplished by opening the oil reservoir cap and
allowing the pump to gulp air for a few seconds. A
mechanical pump pressure of 0.1 Torr or higher after
purging is an indication that an oil change is required.
A clean mechanical pump operates at 0.01 - 0.05
Torr. Unreliable pressure measurements can result
from dirty contacts on the pressure gauge switch. Spray
contact cleaner should be used as required to insure
accurate pressure measurements.
The mechanical pump oil level gauges should be
inspected periodically and cleaned if necessary. Soak
the tubes in acetone for 30 minutes, rinse with
methanol, and dry with a heat gun. Some pumps have
small windows instead of tubes for observing oil levels.
These cannot be cleaned. Tygon vacuum lines may be
cleaned with methanol but not with acetone which
dissolves Tygon. This should be done whenever the oil
is changed and the lines should be inspected for soft
'spots or wear, particularly at the connection points.
The metal tube connecting the pump to the separator
should be cleaned at the same time since oil can collect
in the horizontal part of the fitting and contribute to a
high background. Metal fittings may be washed with
acetone and rinsed with methanol.
Mechanical pump belts should be checked for
correct tension and wear at least every six months or
any time the system is shut down. A correctly adjusted
belt can be twisted 90 degrees. The rough pump belts
often give a warning signal when they start to fray or
develop cracks prior to breaking; they usually develop a
noise and the operator should be aware of any change
in the sound of the pumps. If the pump guards are
removed and left off, it is much more conducive to
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regular checks on the condition of the belts.
Special attention should be given to oil leaks if they
develop. On direct drive pumps the motor to pump
seals may be replaced if necessary.
DIFFUSION PUMPS
Oil changes are required for diffusion pumps and the
considerations for the frequency of changes are the
same as discussed under mechanical pumps. In general,
diffusion pump oils should remain cleaner than
mechanical pump oils because the mechanical pumps
are at the end of the vacuum system. Diffusion pump
oil can be used for up to three years if the pressure
remains good and the background low. Use Santovac
No. 5 oil (a polyphenyl ether made by Monsanto) in
the main' analyzer diffusion pumps. This oil has a very
low vapor pressure and its background contribution is
negligible. A silicone oil such as Dow-Corning 704 or
705 is used in the smaller diffusion pump attached to
the batch and direct inlet systems. This oil has a greater
resistance to oxidation and is better suited to the inlet
systems where oxygen pressures may be high.
Whenever a diffusion pump oil is changed, the old O-
rings should be replaced. Tygon tubes should be
inspected and cleaned as described under mechanical
pumps.
The cooling water exit!, of the diffusion pumps
should be checked daily for proper flow. Occasionally
solid particles from corrosion plug the exit fittings from
a pump and cause it to overheat. This is more likely to
happen in an older system. If flow is bypassing one
pump, the cooling coils will be hot to the touch. The
cooling water lines should be cleaned whenever the
pump oil is changed. A complexing agent such as
EDTA (Versene) or other commercial cleaning agents
work well for this. If cooling water is 50 ppm calcium
hardness or higher, lines will plug within two years if
not cleaned. If the cooling water has a high sediment
content, a reliable sediment filter is recommended for
the cooling water line. This filter should be maintained
regularly to prevent reduced flow rates.
ION GAUGE, MANIFOLD, AND
INLET SYSTEMS
The Bayard-Alpert ion gauge should be outgassed
daily for approximately five minutes. The ion gauge
may be wrapped in aluminum foil to increase the
temperature of the tube. This helps keep the gauge
clean and expedites outgassing. Some Finnigan models
are fitted with an aluminum protective cover for the ion
gauge. This also serves as a reflector to increase the tube
temperature. If this shield is" not provided, it is a good
idea to build a plexiglass cover for the ion gauge. A
dropped tool and a suddenly shattered ion gauge tube is
a catastrophic event.
The manifold may be baked out occasionally at
200-250C if background is a problem. The magnet
should be removed and the ionizer and electron
multiplier potentials should be turned off. In the event
of extreme contamination, the manifold can be cleaned
with acetone or methanol.
If the direct inlet system is used frequently, pump oil
can backstream and settle in the solid probe area and
contribute to background. The direct inlet manifold
may be cleaned with a cotton swab dipped in acetone or
methanol. However care must be exercised in baking
the system since the direct inlet valves contain Viton O-
rings. These O-ring seals should be replaced at regular
intervals if the direct inlet system is used frequently.
The metal disk filter between the GC column and the
separator must be cleaned if the gas chromatograph is
operated at high temperatures. The frit is cleaned with
methylene chloride in an ultrasonic bath.
The manifold, batch inlet, transfer line, and
separator oven temperature monitoring systems must
be verified occasionally with a reliable thermocouple
and a good external potentiometer. The contacts on the
temperature switch should be cleaned with an abrasive
paper and spray contact cleaner to insure accurate
temperature readings.
The batch inlet system septum should be changed
each time the system is brought to atmospheric
pressure.
8.2 THE MASS SPECTROMETER
ELECTRONICS
COOLING FANS AND DUST FILTERS
With modern solid state electronics the single most
important preventive maintenance factor is the flow of
cool air across and around electronic components.
Clean dust filters and working fans provide these flows
and it is absolutely essential to maintain them properly.
The proper operation of cooling fans is extremely easy
to check and this should be done once a week. The time
interval for cleaning cooling fan filters varies widely
depending on location and the air quality in the mass
spectrometer laboratory. Frequent checks of air flows
and the cleaning of filters quarterly is essential.
The Finnigan model 1015 has cooling fans with
filters on the oscilloscope, RF/DC generator, and
power supply modules. A fan without a filter is
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contained in the oscillographic recorder. Other models
have a similar placement of fans and filters.
VACUUM TUBES
The older Finnigan model 1015 systems have in
excess of 25 vacuum tubes and the 3000 series
instruments have four vacuum tubes in the RF/DC
generator (one 6AL5,one 6EB8, and two 8458).There is
wide disagreement about changing vacuum tubes on a
regular basis in any preventive maintenance program.
One extreme philosophy is to never change a tube until
unstable operations or failures occur. At that time
tubes are prime trouble shooting targets. It is more
prudent to regularly change tubes and the schedule
suggested in this manual is intended as a guideline for
the 1015 system.
RF/DC Generator. Replace 5726 and 807 tubes
annually. The 5726 is a 6AL5 replacement.
Oscilloscope. Replace the 68Q6 tube annually.
Electron Multiplier Power Supply (Keithley).
Replace the 8068 and OA2 tubes annually.
Low Voltage Power Supply (Dressen-Barnes).
Replace the 6AV6, OA2, 12AX7, 655OA, and
5R4GYB tubes annually. Check 655OA and 5R4GYB
tubes semi-annually.
Low Voltage Power Supply (Finnigan). Replace the
6LQ6, OA2, and 12AX7 tubes annually.
Oscillographic Recorder (Century). Clean the
optical surfaces annually. These are cleaned in place
with a cotton swab and alcohol; wipe clean with a
tissue. Check the condition of the drive belt and the
galvos annually.
8.3 THE GAS CHROMATOGRAPH
The GC septum should be changed weekly. The oven
and injection block temperature monitoring systems
must be verified occasionally with a reliable
thermocouple and a good external potentiometer. The
dirt filter should be cleaned regularly. The utilization of
drying agents, filter traps, and an oxygen scrubber is
recommended for the carrier gas line, and these should
be regenerated or replaced as necessary.
8.4 THE DATA SYSTEM
SOFTWARE
Computer programs are called software because they
can be changed relatively easily in contrast to the
resistors, transistors, and integrated circuits of the
hardware. This capability of relative ease of change of
software can provide enormous flexibility and the
.possibility of continuous system updating and
improvement. It also can create a chaos of magnetic
tape and disk cartridges whose contents are all different
and unknown to the user.
The very first consideration of software preventive
maintenance is an organized, systematic method of
dating and labeling all paper tapes, magnetic tapes, and
disk cartridges. Similarly all documentation, which
may be received as loose update sheets, should be dated
and stored in a single file for ease of reference. All
operating system software should be duplicated before
any attempt is made to run the programs. Instructions
for duplicating system disk cartridges, OS-8 disk
cartridges, and Dectapes are given in chapter 7. It is a
sound policy to make several copies of important disks
and tapes and place one copy of each in a secure
cabinet. These copies should be reserved for ultimate
back-up that is never used for anything except making
copies.
COOLING FANS AND DUST FILTERS
The considerations discussed in section 8.2 are
equally applicable to the data system. The PDP-8 data
system contains numerous fans and filters.
All floor standing cabinets contain a double fan and a
large filter at the rear cabinet base. The disk controller
and disk controller power supply modules also have
fans and filters. The PDP-8 has an internal fan and
filter. The Dectape drive and its power supply have
cooling fans. The Houston plotter has a cooling fan and
the Tektronix 4610 hard copy unit has a dust filter. The
System Industries digital interface has a cooling fan
and dust filter. The RIB interface has no fan or filter.
LUBRICATION OF MECHANICAL
PARTS
Because of the mechanical complexity of the
teletype, an annual service call or service contract is
recommended. If service is not readily available, the
motor should be oiled, the motor gears greased, the belt
checked, and dashpot and dashpot cylinder cleaned
and reoiled at least annually. It is recommended that
the teletype be turned off at all times when not in actual
use.
The plotter's sliding metal surfaces should be
cleaned quarterly with isopropyl alcohol. Do not oil or
grease any moving parts or sliding surfaces; all moving
parts are permanently lubricated or made of low
friction combinations. .
The slide mechanisms of electronic modules may be
lubricated with machine oil or graphite as needed.
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MAGNETIC STORAGE DEVICES
The read/write heads of the magnetic tape and disk
drive units must be kept clean and free of dirt and iron
oxide. The tape heads are readily cleaned with
isopropyl alcohol and a soft tissue monthly. The disk
drive heads should be cleaned semi-annually with
isopropyl alcohol and' a lint free wiper. Further
information is contained in the disk drive manual.
DIAGNOSTIC COMPUTER PROGRAMS
Certain diagnostic tests are utilized for
troubleshooting, and several of these are recommended
for checking the integrity of the system on a routine
basis. These tests are explained in detail in chapter 9.
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CHAPTER 9
TROUBLE SHOOTING
Trouble shooting is often the most difficult and
frustrating part of operating a computerized GC/MS
system. The failure of an extremely simple component
or electrical connection .may be the cause of a complete
failure of the system. However, because of the
complexity of the total system, it may be extremely
difficult to isolate the simple problem.
The purpose of this chapter is to develop a systematic
method of trouble shooting a computerized GC/MS
system. As in other chapters, some sections are
oriented to Finnigan model 1015 and 3000 series
quadrupole mass spectrometers with data systems that
employ Digital Equipment Corporation model PDP-8
computers. However, the overall systematic approach
is applicable to any GC/MS system.
The chapter is divided into five sections. The order of
the sections is the same as the probable order of
discovery of problems by an operator following the
recommended operational procedures in chapter 2.
Within each section the problem solving approach is
the same. The first things to look for are simple, easy to
fix problems such as loose or broken cables, blown
fuses, dirty PC board connections, inoperable cooling
fans, dirty dust filters, water or oil leaks, air leaks, and
uncontrolled heaters. If this fails to locate the
difficulty, it is necessary to isolate the problem as much
as possible to a specific module or modules. Once this is
accomplished, manufacture's service manuals should
be consulted to determine specific remedies. It is
beyond the scope of the manual to catalog a large
number of specific failures and remedies. There are
simply too many variations in hardware even within
one manufacturer's product line. If the manufacture's
service manual does not provide a solution to the
problem, it is then appropriate to call a service engineer
for the specific module that is suspect.
9.1 MASS SPECTROMETER
PROBLEMS
VACUUM SYSTEM
There are several warning signals that should be
checked each day on entering the mass spectrometer
laboratory. A diffusion pump over heat light will come
on if the cooling water flow was too low or the water
insufficiently chilled to maintain the pumps at a proper
temperature. A Fenwall switch senses the temperature
at each diffusion pump and automatically shuts off the
high vacuum system in the event of overheat. If the
overheat is limited to just one diffusion pump, the
entire system is shut down. The remedy for this
problem is clearly to adjust the cooling water flow to a
correct level and to assure that the outlet stream is cool.
The Fenwall switch may require resetting before the
high vacuum system is reactivated. See chapter 2 for
the pump down procedure.
Another warning signal is the illumination of the
pressure failure light or an indication of an abnormally
high pressure on the vacuum gauge. With the GC
column disconnected or the carrier gas diverted from
the mass spectrometer, a pressure of 5x10"' to 10"'
Torr should be maintained. Under these conditions air
leaks are insignificant and the presence of ions of
masses 18,28,32, and 40 are of no consequence. If the
pressure becomes sufficiently high, about 10"1 Torr, the
high vacuum system will be shut down. The most
common causes of vacuum system failures are a broken
belt on a mechanical pump, a break in a Tygon or glass
vacuum line, or a leaking O-ring or Teflon ferrule.
Teflon ferrules flow when hot and the metal fittings
need to be tightened occasionally. Electrical problems
may also cause high vacuum system failures. A
momentary power failure will shut down the high
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vacuum system but the mechanical pumps will restart
when the power returns. A blown fuse or a faulty
component on the ion gauge controller board may also
cause'a pressure failure.
For abnormally high pressures that do not shut
down the vacuum system, the first remedy is to tighten
metal fittings containing Teflon ferrules about one-half
turn. If this fails to eliminate the leak, inert gas such as
argon or helium should be sprayed around fittings,
gaskets, tube connections, and O-rings. The
observation of a sudden increase in pressure is an
indication of a leak. If this procedure fails to detect the
leak, turn the ionizer and electron multiplier on and set
the first and last mass controls to display the prominent
ions from the inert gas. Continue spraying the gas and
look for a sudden increase in ion abundance at the
characteristic masses. It may be necessary to change a
gasket or leaking O-ring.
ION GAUGE
The glow of the Bayard-Alpert tube is an indication
of the state of the vacuum system. If the tube glows
extremely brightly, flickers intermittently, or flickers
rapidly when the solvent from a GC injection reaches
the manifold, trouble is indicated. Similarly, if the high
vacuum gauge seems insensitive to changes in pressure
as during solvent elution or the admitting of PFTBA,
the ion gauge should be serviced.
Intermittent flickering may be caused by
contamination from solvents or pump oil. Degassing
overnight may help as will the application of external
heat with a heat gun. See also chapter 8 for preventive
maintenance measures. For other problems, the ion
gauge controller board should be examined for bad
components. If this fails to solve the problem, replace
the vacuum tube.
HEATERS
Manifold, separator, transfer line, or batch inlet
heaters may lose control and overheat. If this occurs,
the respective triac controllers are suspect and should
be tested and replaced. If higher than normal
potentiometer settings are required to maintain
temperatures, one-half of a clamshell heater may be
burned out. Also, bad thermocouples and dirty meter
switch contacts cause inaccurate temperature readings.
9.2 DATA SYSTEM PROBLEMS
Many data system problems are caused by simple
failures that are readily corrected. Power cables and
signal transmission cables may work loose and all such
connections should be checked at the first sign of
trouble. Similarly fuses, cooling fans, and filters should
be checked at once. Some modules have normal/test
switches and if a switch was inadvertantly left in a test
position, the module may not funtion normally.
Magnetic read/write heads should be cleaned as
described in the preventive maintenance chapter. If
software on a disk or tape was altered by some
malfunction or accident, programs may suddenly fail.
An alternative disk or tape of known good quality
should be tried. If these measures fail, it is advisable to
check all PC boards for secure, tight, and clean
connections. It is worth lifting each PC board in a unit
from its connector, removing dirt corrosion with an
ordinary pencil eraser, and replacing each board.
Electronic component and some mechanical failures
are best found with the use of a diagnostic computer
program. The programs in the following sections are
for the PDP-8 data system, but comparable programs
should be made available by each data system
manufacturer. After isolation of the particular problem
with the diagnostic program, it is appropriate to call a
service engineer for the faulty module.
COMPUTER DIAGNOSTIC PROGRAMS
A large number of computer diagnostic programs
are available for the PDP-8 from the Digital
Equipment Corporation. Each of these programs tests
the operation of one or several computer functions.
Digital Equipment Corporation maintenance and
diagnostic programs are recognized by the
characteristic name, MAINDEC, followed by a series
of digits and letters. Each progam is supported by a
document that describes the use of the program and the
error messages that are printed. These documents are
required to gain full advantage of the diagnostic
programs.
The most important decisions that must be made
when trouble shooting the data system are which
diagnostic program to run and when to call the service
engineer. In general it is possible to save considerable-
time and expense by running diagnostics to isolate the
problem before calling a service engineer. Reporting
the results of the diagnostics at the time the service call
is made sometimes allows a quick solution to the
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problem by replacement of a specific printed circuit
board. In a few cases the choice of a diagnostic program
is quite clear. For example, if a problem repeatedly
occurs when using a magnetic tape drive and only when
using the tape, find a diagnostic for the magnetic tape
system and run it. Dectape diagnostics are discussed in
the next section of this manual. If all the more readily
recognized device problems are eliminated, the
magnetic disk system is the next peripheral to check
since it contains mechanical funtions that are more
susceptible to failure than the purely electronic
functions of the computer itself. The disk diagnostic
program is described in a subsequent section and it is
not a standard Digital Equipment Corporation
program. The PDP-8 disk system employs a Diablo
Corporation series 30 moving head disk drive and a
controller manufactured by System Industries. The
diagnostic program was written by System Industries
and it has its own detailed documentation.
If it is determined that the disk system is functioning
properly, it is appropriate to run computer diagnostics.
Table 9.1 contains a list of OS-8 program names for a
selection of computer diagnostic programs, brief
operation instructions, and the satisfactory test
indications. This list is a small subset of the total
number of available computer diagnostics, but it
includes some of the most general tests that are
recommended for reasonably comprehensive testing of
most basic computer functions. It is strongly
recommended that the GC/MS operator run several or
more of these programs at regular intervals in order to
become familiar with their correct operation. With
systems that are not used often, these programs should
be run regularly to exercise the system and keep it in
good operating condition. With these diagnostic
programs stored on the OS-8 operating system, it is
easily possible to test the computer's function in a few
hours. If the complete program documentation is not
available, it is possible to gain some valuable
information with the general directions that are given
in Table. 9.1. To load the programs from the OS-8
system, enter R, then a space, and the name of the
diagnostic program. The programs should be run in the
sequence shown in Table 9.1 since some of the later
tests assume correct functioning of earlier tests. All
programs have the standard .starting address 0200 if it
is necessary to restart them. The programs are stopped
by pressing the HALT switch. The XADDR,
XCHKBD, and EAEXME programs require at least
8K of memory, but there are corresponding programs
for 4K systems. Error messages are printed in the event
errors are found, and the complete program
documentation is required to interpret the error
numbers. The error number explanations may have
little meaning to most operators, but should be
available before calling a service engineer. After halting
the program, OS-8 may be restarted at address 7600.
However .the two memory diagnostics write over all
contents of memory, and the OS-8 bootstrap must be
reloaded to restart OS-8 in these cases.
Table 9.1 Computer Diagnostic Programs for the PDP-8/ E or M
OS-8
Program Name
INST1
INST2
XADDR
Function
CPU instruction
tests
CPU instruction
tests
extended memory
address tests
Operation
halts on loading; enter 7777
in switch register and press
clear and continue
starts-on loading
halts on loading; enter
starting address 0200 in
switch register, press load
address, clear, and continue;
halts and prints message;
enter in the switch register
0001 for 8K, 0002 for 12K,
etc. and press continue
Satisfactory
Test Indication
bell every few
seconds
bell every few
seconds
prints the numeral
5 every five minutes
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Table 9.1 Computer Diagnostic Programs for the PDP-8/E or M (continued)
OS-8
Program Name
XCHKBD
Function Operation
extended core halts on loading; enter in
memory tests the switch register 0200,
press load address, clear
and continue; halts and prints
message; enter in the switch
register 0001 for 8K, 0002
for 12K, etc. and press
continue
Satisfactory
Test Indication
prints the numeral
5 every five minutes
ADDER
CPU adder
circuit tests
EAEST1
EAEST2
EAEXME
extended arithmetic
element instruction
tests
extended arithmetic
element instruction
tests
extended arithmetic
element - memory
tests
starts on loading; before
calling program enter in the
switch register 0210 for 8K,
0220 for 12K, etc and then
call program
halts on loading; enter 0200
in switch register, press load
address; enter 1000 in switch
register; press clear, and
continue
halts on loading; enter 0200
in switch register, press load
address, clear and continue;
halts; enter 0400 in switch
register and press continue
halts on loading; enter 0200
in switch register and press
load address; enter 4000 in
switch register for 4K, 4001
for 8K, 4002 for 12K, etc;
press clear and continue;
after message enter 0 for
4K, 1 for 8K, 2 for 12K, on
the terminal keyboard and
press return
prints the characters
SIMAD, SIMROT, FCT,
and RANDOM after 35
minutes
prints the
characters KLE81
every 6 minutes
rings bell every
minute
prints the
characters KE8 EME
every 22 seconds
For problems that are intermittent, it is
recommended that one of the memory or general
instruction test programs be permitted to run
overnight. Raising the temperature of the room during
testing is a method of causing marginal components to
fail completely.
A complete list of the MAINDEC diagnostic
programs is found under acceptance tests in the Digital
Equipment Corporation PDP8/E, PDP8/F and
PDP8/M Processor Maintenance Manual - Volume 1.
Additional tests for modules not included in Volume 1
are found in Volume 2, Internal Bus Options or in
Volume 3, External Bus Options, in Volumes 2 and 3
the available MAINDEC programs are usually listed
under Software, Acceptance Tests, Maintenance, or
Trouble Shooting. Lists of maintenance and diagnostic
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programs are also found in other Digital Equipment
Corporation publications. For example a list is found in
appendix A of the 1971 edition of the PDP8/E Small
Computer Handbook.
DECTAPE DIAGNOSTIC PROGRAMS
The Dectape diagnostics are described separately
because problems may be readily identified with this
unit when failures occur only during Dectape
operations. Also included is a relatively simple tape
drive brake ajustment that is a solution to several
problems.
There is one aspect of Dectapes that causes
confusion. All Dectapes are not alike although they
may appear physically identical and data files and
programs may be transferable between them. The most
common Dectape drive is the TU56 in either a single or
double tape drive configuration. The confusion arises
because this drive is used with the relatively slow TD8E
interface board and the relatively fast TC08 Dectape
controller. The TD8E and the TC08 are not compatible
and Dectape access programs written for one will not
work with the other. Each controller has a different
format program and different diagnostic programs but
data files and non-Dectape programs are fully
compatible with each system. To add to the confusion,
older documentation often refers to the older TU55
tape drive and TC01 Controller which are very similar
totheTU56andtheTC08.
The diagnostic programs for Dectape units are listed
in the appropriate maintenance manual, e.g., the TC08
Dectape Controller maintenance manual under
Software. If a Dectape is suspected of causing
transmission errors or exhibits sluggish performance,
an exerciser program should be run. A random
exerciser program called TC08RX is available for the
TC08 Dectape controller. A program called TD8DIA
is available for TD8E Dectapes. The use of the TD8E
test program requires the complete program
documentation and this program is not discussed here.
The following information refers to the TC08 test
program, but TD8E users should take note of the TU56
brake drive adjustments and other comments in the last
two paragraphs of this section.
After the program is loaded into memory, the
computer will halt. Mount a formatted Dectape on the
drive or drives to be tested. More than one drive may be
tested at the same time if desired. The tape or tapes
must not contain any data or programs that are needed,
as the diagnostic destroys all information on the tape.
Set the desired drive number using the thumbwheel
switch on the Dectape drive and place the unit in write
enable and remote. Load the starting address of the
program, 0200, into the switch register and press
LOAD ADDRESS. Set the switch register to select the
drive or drives to be tested as shown in Table 9.2.
Table 9.2. Switch Register Selection of Dectape
Unit in the Random Exerciser Test.
Dectape Unit on
Thumbwheel Switch
0
1
2
3
4
5
6
7
Octal Value of
Switch Register
4000
2000
1000
0400
0200
0100
0040
0020
Several drives may be tested at one time by combining
the switch register settings for the corresponding
Dectape drives. Press CLEAR and CONTINUE
switches. The program will halt again. Place 0000 in
the switch register and press CONTINUE. To halt the
test, press the HALT switch. The complete program
documentation is required to interpret the error
messages and use all program options.
Errors will be found if a read/write head is dirty, the
tape is badly worn, or the unit is overheating due to an
inoperable cooling fan. A worn tape may be reclaimed
by reformatting. It is recommended that the first five
feet of a worn tape be removed before reformatting.
This may eliminate the most worn section. Other errors
may be due to an incorrect tape drive motor brake
adjustment. This undesirable situation can also be
observed by sluggish performance of the tapes on stops
and turn arounds. This problem can wipe out existing
files on a tape or make it impossible to store sample
data.
To correct this problem on a dual transport TU 56
tape unit, there are two adjustments on printed circuit
board M302 which is the dual delay motor voltage. The
bottom trimpot adjusts the right transport and the top
trimpot adjusts the left transport. Whether the pots
should be turned clockwise or counterclockwise
depends on which motor is most out of adjustment. The
adjustment is most easily made if one person operates
the transport manually while the second adjusts the
trimpot. Adjust voltages until stops and starts are crisp.
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DISK DIAGNOSTIC PROGRAM
This extremely important program has several
functions and it is described separately for the reasons
given in the section on computer diagnostics. The
program's functions include formatting new disk
cartridges, testing the surface of the magnetic disk,
testing the functions of the disk drive, and testing the
disk controller. If any errors are found, an error
number is printed. The error numbers and explanations
of the malfunctions are listed in the System Industries
disk maintenance manual. These error numbers and
explanations have little or no meaning to the average
operator, but it is important to run the diagnostic
program and have the error message ready before
calling a service engineer.
The disk diagnostic program is named DDIAGN
and it may be loaded into the computer from an OS-8
disk as indicated below. In the following discussion, the
SWR refers to the switch register on the PDP-8 front
panel. The first prompt printed by the disk diagnostic
program is:
ENTER DISK TEST INFORMATION
After this and all other prompts, the computer halts
(the run light goes out). The procedure followed is the
same for all prompts: Enter a twelve digit binary
number into the SWR and press the CONTINUE
switch on the PDP-8 front panel. In the instructions
that follow the twelve digit binary number is expressed
as a four digit octal number. The sample dialogue is
recommended for most purposes, but some optional
responses to several prompts are discussed below.
Insert and start the OS-8 disk.
.R DDIAGN
ENTER DISK TEST INFORMATION
Before responding to this prompt, remove the OS-8
disk and insert a new or test cartridge. Enter 300x into
the SWR where x = the disk unit number ( 0 for a
single disk drive, 1 for the second unit of a two drive
system, etc.) and press continue. If more than one drive
is present, more than one test can be started at the same
time as follows:
ENTER DISK TEST INFORMATION
(enter 3000 and press continue)
ENTER DISK TEST INFORMATION
(enter 3001. and press continue)
ENTER DISK TEST INFORMATION
(enter 0000 and press continue)
ENTER UNIT ADDRESS
(enter 0050 and press continuej
ENTER FORMAT LOOP CONTROL
(enter 0000 and press continue)
ENABLE FORMAT SWITCH, ERROR AND
TYPE OUT CONTROLS
(enter 0002 and press continue)
UNIT 0
UNIT 1
DISABLE FORMAT SWITCH
UNIT 0
UNIT 1
UNIT 0
UNIT 1
UNIT 0
UNIT 1
UNIT 0
Each time the unit number is printed a new cycle of
tests begins for that drive. Note that any and all
programs or data stored on the test disk will be
destroyed. One of the prompts printed is:
ENTER FORMAT LOOP CONTROL
If a 0000 is entered, the disk will be formatted once at
the beginning of the first pass of the tests. On
subsequent passes, the disk will not be reformatted.
Any non-zero entry will cause the program to reformat
the disk before every pass of the tests. A single
formatting is adequate and 0000 should be entered. The
last prompt printed is:
ENABLE FORMAT SWITCH, ERROR AND
TYPEOUT CONTROLS
Several responses to this prompt are possible to
perform a variety of functions. Place the format enable
switch on the rear panel of the disk controller in the
format position, enter one of the following codes into
the switch register, and press CONTINUE. Code 0002
is recommended for most situations and is especially
suited to over-night testing for intermittent errors.
0002. Causes the disk to be formatted and runs
diagnostics. If an error occurs, an error
message is printed and the program continues
with the next test. At the conclusion of all tests
the sequence of tests is repeated. The program
runs about one hour with the format switch
enabled and completes one cycle of tests in
another hour with the format switch disabled.
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0000. Causes the disk to be formatted and runs
diagnostics. If an error occurs, an error
message is printed and the program halts.
Running time is the same as 0002.
0003. This entry is used following a halt with 0000.
Enter 0003 and press CONTINUE and the
diagnostic will continuously repeat the test
that caused the error.
. 0040. This is a fast format option. The disk is
formatted in about two minutes and the
program halts without requesting the user to
disable the format switch. This option is
acceptable in emergency situations when a
formatted disk is required immediately. It is
not recommended in general as all disks should
be thoroughly tested after formatting.
To stop the test, press the HALT switch. The OS-8
disk may be reinserted and the OS-8 system restarted at
address 7600. Alternatively a new test disk may be
inserted and DDIAGN restarted at 0200.
9.3 SYSTEM ZERO ADJUSTMENT
PROBLEMS
If the system zero adjustment described in section
2.4 cannot be achieved, or if the signal is excessively
noisy, there are several likely causes. Instabilities are
sometimes caused by overheating of electronics due to a
cooling fan failure or a dirty filter that blocks the
passage of an adequate amount of cool air. Vacuum
tubes in the RF generator (1015 and 3000 series) and
power supplies should be checked or replaced. The
preamplifier may be faulty and zeroing should be
attempted on all of the preamp ranges. If possible swap
the preamp for a spare and attempt to zero. Some
preamplifiers have a coarse zero screwdriver
adjustment. Set the fine zero pot to mid-range and
adjust the coarse zero using the ZERO program. Some
preamplifiers have a screwdriver hum balance
adjustment. Consult the manufacturers manual for
details of this adjustment.
The other potential major problem area is the mass
spectrometer interface. The proper functioning of the
interface is best tested using the interface diagnostic
program described in section 9.4. If the diagnostic
program indicates the interface is functioning properly,
yet it is not possible to zero, the fault may be a noisy
electron multiplier. Before replacing or reconditioning
the multiplier, refer the subsequent sectionsjrtcluding
LOSS of IONS. As with many other problems, failure
to zero properly also suggests a dirty ion source.
9.4 MASS SCALE CALIBRATION
PROBLEMS
The automatic mass scale calibration program
should complete a successful calibration of the mass
range 20-650 amu at a PFTBA pressure of about 1 X
10"* Torr in about 40 seconds or less. If a longer time is
required, or the system will not calibrate, moderate to
serious trouble is indicated. There are a very large
number of potential causes for mass scale calibration
problems and it is simply not possible to describe each
in detail. Therefore a general approach to the diagnosis
of the problem is given here and the manufacturer's
maintenance manual should be consulted for specific
details.
After a calibration failure, the system tune-up should
be checked following the procedure in the section 2.2.
During this tune-up check it may not be possible to
observe any signals from PFTBA ions. This is classified
as a major problem and one should check the next
section titled LOSS OF IONS. If ions are observed the
calibration problem should be attacked in the following
manner.
If the calibration diagnostic program described in
section 2.5 was routinely applied, past records should
be examined for signs of day to day drift. The vacuum
.tubes in the RF generator, particularly the 6AL5 or its
5726 replacement option, are prime suspects in cases of
calibration drift. Problems with these tubes may not be
observed with a vacuum tube checker. A new tube
should be inserted and its stability determined
experimentally. If drift continues, try several new tubes
and select the most stable one of the group. The
Finnigan 3000 series instruments have four vacuum
tubes including a 6AL5 in the RF generator.
A drift in an RF tuning capacitor can cause
calibration problems. This capacitor compresses or
expands the mass range observed during a single sweep
of the rod voltages. There is one tuning capacitor for
each range on the 1015 and a single tuning capacitor for
the 3000 series mass range. The proper adjustment of
the tuning capacitors is described in the first mass, last
mass calibration procedures in the Finnigan 1015
operator's manual. A similar procedure exists for the
3000 series spectrometers.
A problem in the mass spectrometer interface can
cause calibration failures. The proper functioning of
the interface diagnostic program is described in a
subsequent section of this chapter. Another valuable
program for diagnosing instability problems is the peak
profile diagnostic program which is also described in
131
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this chapter. Again a dirty ion source may be the cause
of a calibration failure.
INTERFACE-SPECTROMETER
GAIN ALIGNMENT
Calibration problems with the Finnigan 1015, 3000,
and 4000 mass spectrometers could be caused by
incorrect alignment with the' PDP-8 interface. The
System Industries (SI) interface outputs 0-10V which
corresponds to 1-750 amu or 1-1000 amu. The amu
range is handled by the driver file. The standard
calibration driver file that is built into the calibration
program is set up for 43 digital to analog converter
(DAC) units per amu (43 x 750 = 32,250). The 15 bit
DAC has a range of 0-32,768 DAC units. The FC1000
and Ml000 driver files are set up for 32 DAC units per
amu (32x1000 = 32,000).
The problem that develops is that the 0-10V range of
the SI interfaces have to be matched with the 0-10V
range of the Finnigan mass spectrometers. The
calibration files work as follows. The driver files consist
of a list of DAC ranges that correspond to the
calibration masses. The DAC ranges cover +3 amu
around ,the calibration mass. For example in the
standard driver file mass 100 has a DAC range of 43 x
100 = 4300 DAC units + (3 x 43 =) 129 DACunits;
in otherwords mass 100 + 3amu corresponds to the
range of 4171-4429 DAC units. The SI interface
outputs i the 4171-4429 DAC unit range which
corresponds to 1.2728-1.3516V sent to the
spectrometer. The most important idea is that the mass
100 peak must be in this range and all other calibration
masses must be in their ranges. On the Finnigan 1015
R-73 on PCS is an offset adjustment to make mass 100
fall in the correct range.
If the Finnigan ramp voltage (PC-5 on 1015.) is set up
so that mass 100 is passed through the quadrupole at
1.262 volts, calibration will fail because the SI interface
and calibration program look for mass 100 between
1.2728-1.3516V. R-73 (on the 1015) shifts the ramp up
or down without changing the slope. Thus the
spectrometer may be set up so mass 100 will be passed
through the quadrupole in the correct voltage range.
A problem was created when Finnigan eliminated
the R-73 adjustment in the 3000 and 4000 series mass
spectrometers. R-73 may be thought of as a very coarse
resolution, coarser than R-74. To compensate there is a
"MASSOUT GAIN" pot in the new RIB interface.
This allows matching of the interface ramp with the
instrument ramp. To make this adjustment run the
peak profile diagnostic program MSSCAN, which is
described in section 9.4 and introduce PFTBA. Center
mass 100, or 219, or etc. on the screen with about a 500
DAC unit range. Then calculate where the peak should
be in DAC units as follows: 1-1000 amu instruments:
mass x 32 DAC units = ; 1-750 amu
instruments : mass x 43 DAC units =
Using MSSCAN determine where your peak is, and
adjust R-73 on the 1015 or the MASSOUT GAIN on
th RIB until the mass is centered about- where it should
be. Remember there is a +3 amu (+ 96 or 129 DAC
unit) range in the calibration file.. The user should be
aware that the MASSOUT GAIN pot may be mounted
over the letters SSOUT; therefore it looks like MA
GAIN on the label in the RIB interface.
LOSS OF IONS
If no ions are observed during an attempted tune-up,
the first check is the 0-200V ramps. On the model 1015
these are observed at TP5 and TP6 on PCS (see Figure
2.1). On the 3000 series instruments the ramps are
observed at TP4 and TP5 on RF/DC control card. If
the ramp is present the loss of ions is probably due to a
failure in the ion source, electron multiplier, or one of
their power supplies. A non-existent ion source
collector (trap) current suggests a broken filament: a
lower than normal trap current suggests a sagging
filament that must be replaced. If source potentials are
missing or low in value, the problem may be on the ion
source control PC board. The electron multiplier
power supply output should be checked. Some power
supplies have vacuum tubes that should be replaced
regularly. See chapter 8 for a recommended
replacement schedule.
Another good trouble shooting approach is to shut
down all power to the mass spectrometer and check all
electrical leads to the ionizer and multiplier for
continuity or no continuity as appropriate. Consult the
manufacturers maintenance manual for specific
directions. If shorts are indicated it will be necessary to
remove the ionizer and multiplier assemblies from the
manifold and check for shorts and correct assembly.
If the -200V ramp was not present, check TP20 on
PCS of the 1015 for the ramp. Check TP1 and TP6 on
the RF/DC control board of the 3000 series
instruments. If this is present the problem is probably a
component on the PCS board or the RF/DC control
-board.. If the ramp is not present at TP20 (TP1/6)
check the output of the +1200V and +200V power
supply. Vacuum tubes should be replaced if necessary.
Also there are vacuum tubes in the RF generator of the
1015 and 3000 series instruments. See chapter 8 for
more details on these.
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INTERFACE DIAGNOSTIC PROGRAMS
Problems in the mass spectrometer interface are
often revealed during an attempt to calibrate or during
operations with an apparently acceptable calibration.
The interface diagnostic program is an excellent
approach to finding interface problems. It is a good idea
to run the interface diagnostic program at regular
intervals as a preventive maintenance routine when the
GC/MS system is not in use. This will exercise the
electronic components of the interface and familiarize
the operator with the method of running the program.
There are two versions of the program that
correspond to two models of the interface. Both models
perform identical functions, but the later model takes
advantage of advances in solid state technology and is a
smaller overall package that may be somewhat remote
from the data system. This interface is often called the
remote in base (RIB) interface. The interface diagnostic
programs are identified with hardware as follows:
OK
OK
OK
OK
(after completion of test, place manual
test switch in off position)
.R NEW150
DO YOU
DO YOU
NO
DO YOU
DO YOU
YES
DO YOU
TEST?
DO YOU
WANT STATIC TEST? NO
WANT TRANSMISSION TEST?
WANT ANALOG ADJUST? NO
WANT MASS SPEC TEST?
WANT REMOTE SEQUENCING
YES
WANT IFSS TEST? YES
Interface Model Number Interface Diagnostic Program
1152-7016 (separate analog
and digital drawers)
5000-7073 (RIB or remote interface)
MSTEST
NEW 150
The interface diagnostic programs are stored on the
OS-8 system and may be loaded into the computer as
described in the previous section on computer
diagnostic programs. Both programs have a starting
address of 0200. For general trouble shooting surveys,
operator familiarization, and interface exercising, the
followiing responses to the prompts are strongly
recommended:
R MSTEST
DO YOU WANT STATIC TEST? NO
DO YOU WANT MASS SPEC TEST?
YES
DO YOU WANT OFFSET ADJUST
PROMPT? NO
DO YOU WANT TRACKING ADJUST
PROMPT? NO
DO YOU WANT IFSS TEST? YES
DO YOU WANT PLOTTER TEST? NO
PUT LOGIC DRAWER IN TEST MODE
(place manual test switch on back of
logic drawer in ON position)
(press continue)
DO YOU WANT PLOTTER TEST? NO
OK
OK
OK
The prompts that are answered in the negative refer
to specialized tests and adjustment aids that are best
used after trouble is indicated in the Mass Spec and/or
IFSS tests. It is extremely important to run the IFSS
test since this mode is used during mass scale
calibration. A major advantage of running the
suggested tests only is that after completion of each
test, the program prints OK, then repeats the
diagnostic. Therefore it is possible, and strongly
recommended, to run the test continuously over a long
period of time, including overnight. This will enhance
considerably the chances of finding crucial but
intermittent errors. Be certain to enter 0000 in the
switch register to insure the program will continue even
if an error is detected. To stop the program press the
HALT'Switch.
If an error is detected, the program will prinr an
error message. As usual most of the error messages will
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probably have little meaning to the operator even after
consulting the appropriate System Industries mass
spectrometer interface maintenance manual. However
having the error numbers available when a service
engineer is called could save considerable time and
expense. However, there are several errors that are
related to relatively simple potentiometer (pot)
adjustments that should be attempted by the operator.
Errors 3 and 4 occur if the analog to digital converter
(ADC) zero is not in agreement with the digital to
analog converter (DAC) zero. The zero may be
adjusted by a trial and error procedure until errors 3
and 4 are corrected. Trial and error consists of turning
the zero adjust potentiometer on the right side of the
ADC (Phoenix analog drawer) one-half turn in one or
the other direction while the diagnostic is running and
observing the errors messages. A YES response to the
MSTEST prompt DO YOU WANT OFFSET
ADJUST PROMPT? was intended to facilitate this
adjustment by continuously rerunning the diagnostic
that leads to errors 3 and 4. However there is little point
in continuously rerunning the one specific diagnostic,
since the entire MASS Spec and IFSS tests only require
several minutes. A much quicker method of making
this adjustment in the two drawer interface is to run the
program ADZERO.
ADZERO Program. This program is a modfied
version of the preamplifier zero program, ZERO,
described in section 2.4. It is loaded as follows:
SELECT MODE: ADZERO
MANUAL? N_
AUTOMATIC? N_
ZERO ADJUST? Y_
This program causes the DAC to output zero volts.
This output is then connected (through software) to the
input of the ADC with the ADC's output being
displayed in the accumulator of the PDP-8. If no lights
are visible, turn the zero adjust pot CCW until a light
appears in the accumulator. Rotate the pot CW until
the light goes out completely (stops flickering). At this
point rotate the pot another 1/2 turn CW. This will
insure operation in the safe region of the operating
range. If a light or lights are initially displayed in the
accumulator, eliminate them using the above
procedure.
The small remote interface may require the same
adjustment after an occurrence of the same errors. The
correct pot is labeled integrator offset on the top board
of the interface. The ADZERO program is fully
compatible with the remote interface and may be used
to facilitate the adjustment.
Another error that may be corrected by a simple
adjustment on either interface is error 6. This is caused
by an improper gain pot adjustment. This pot on the
remote interface is labelled the unity gain pot. A trial
and error process should be used during the Mass Spec
and IFSS tests to make this adjustment.
With the excepton of the Houston plotter test, the
other prompts of MSTEST and NEW 150 were
intended to facilitate certain adjustments and
measurements. These are not as generally useful to the
system operator, but may be used if desired. The
System Industries interface manuals describe these
tests. The plotter test may be the most useful of the
remaining tests, but a failure does not necessarily
indicate trouble in the plotter itself. The plotter
interface is contained in the digital bay of the two
drawer interface, and is on a separate PDP-8 board
when the remote interface is present.
PEAK PROFILE DIAGNOSTIC PROGRAM
This program is a valuable tool to investigate
problems of system zero adjustment, calibration,
quality assurance, or intermittent instability. For
example, if the mass scale calibration is failing because
of a weak 6AL5 (5726) detector diode tube in either a
model 1015 or 3000 series, a clear observation of this
instability can be made with the program.
The program gives the operator the capability of
observing repeatedly an entire mass spectrum, a small
portion of a mass spectrum, or a single peak in a
spectrum at the data system CRT. These same basic
capabilities are available at the mass spectrometer
console oscilloscope, but the CRT is easier to use for
diagnostics because of its storage capability. With the
CRT and the program, the operator has a very much
better opportunity to examine clearly the details of
peak shape and its stability. Also since this program
uses the data system, if a spectrum is clearly observed
on the oscilloscope, but not with the program, the
problem is immediately isolated to the data system
itself or the data system-mass spectrometer interface.
The name of the diagnostic program is MSSCAN
and the program is available on the OS-8 and the real
time operating systems. Before the program is run,
perfluorotributylamine (PFTBA) must be introduced
into the mass spectrometer. Turn on the ionizer and the
electron multiplier. Under OS-8 the program is called
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with the command R MSSCAN. Under the real time
system the dialogue is as follows:
SELECT MODE: MSSCAN
CONST, SCAN OR?
A user entry of a question mark causes the program to
print a list of MSSCAN commands that is reproduced
and explained in detail in this section. A user entry of
the command C (not CONST) causes the program to
enter a non-scanning mode. In this mode additional
commands are available as shown below. One may
cause the program, by the various keyboard entries to
set and hold various rod voltages. These voltages are
expressed in terms of the corresponding digital to
analog converter (DAC) units. Also one may print the
corresponding analog to digital converter (ADC) data
after integration of the electron multiplier signal for
various time periods. This constant mode of operation
has some utility for trouble shooting, but is is generally
less useful than the other mode of operation.
The most useful application of the program is the
scanning mode that is entered by the command S (not
SCAN). Subsequent prompts are shown in the sample
dialogue, which should cause mass 219 (from PFTBA
for example) to be displayed near the center of the CRT
screen with a 1-750 amu mass range instrument.
CONST, SCAN OR ?S_
STARTING DAC 9150
RANGE 500
INCREMENT 3_
If the peak is not prominently displayed, any of the
single character commands under the scan mode may
be entered to modify the program scanning conditions.
The screen will be paged automatically, and the
command printed. Enter the new value and scanning
will be resumed. The first command to try is the M
command which multiplies the peak intensity by the
value entered. One may also change the starting DAC,
range and increment slightly since the exact values
required to display mass 219 in the center of the CRT
will vary somewhat from instrument to instrument. In
general one amu corresponds to about 43 DAC units on
a 750 amu mass range intrument and 32 DAC units on
a 1000 amu mass range instrument. A starting DAC of
about 2000, a range of 20000, and an increment of 10
will display the spectrum from about 40-700 amu. To
exit from the program or to recover from an error after
paging the screen manually, enter the E command.
This will return the program to the first prompt. Under
OS-8 enter a CONTROL/C and under the real time
system a CONTROL/L to return to the system
monitor.
MSSCAN Variables
C constant .yoltage (DAC)
S set DAC and read ADC
U increment DAC and read ADC
D decrement DAC and read ADC
P print current DAC
T set time register (max. 4095)
R repeat integration at current register
settings
E back to start
S scan on 4010 display
S change starting DAC
R change range
I change increment
T change time register
P print parameters
O one step each time space bar is pressed
C clear one step - full speed
M multiply intensities
D divide intensities
E back to start
Integration time will be equal to the value in the time
register, in milliseconds. This register is set to 1 at the
start of the program.
The most important observations to make from the
mass 219 ion of PFTBA are peak shape, resolution
from the mass 220 ion, position stability, and
abundance stability. The peak should be symmetrical
without excessive noise or a bra shaped top. Its stability
in position and abundance should be very constant with
little or no movement. It may be necessary to examine a
broader mass range, e.g., 50 amu, to adequately judge
position stability. A noisy or unstable condition is a
clear sign of trouble and a frequent cause of mass scale
calibration failures.
Some of the conditions observed with MSSCAN are
listed below together with a few possible causes of the
problem.
Position Instability: A bad 6AL5 (5726) tube in the
model 1015 or 3000 series RF generator; also three 807
RF tubes are contained in the 1015 generator and two
8458 tubes and a 6EB8 are contained in the generator
of the 3000 series instruments. The power supply for
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the model 1015 has vacuum tubes that can cause severe
instability.
Abundance Instability: A bad preamp; bad tubes in the
electron multiplier power supply or a bad electron
multiplier; a sagging filament or unstable ion source
potentials.
Noisy Peaks: Improper grounding which produces 60
Hz noise in a ground loop; bad power supply tubes or
unstable source voltages. The mass set voltage at TP18
on PC-4 of theFinnigan 1015 should be stable to better
than a millivolt regardless of the source, i.e., internal or
datasystem.
9.5 QUALITY CONTROL PROBLEMS
Quality control problems are defined as problems
that are recognized only when examining the overall
peak size caused by a known amount of DFTPP or by
examining the mass spectrum of DFTPP. At this stage
the system should be tuned and the mass scale
calibrated. The quality control performance evaluation
is conducted as described in section 2.6. Examine the
output from the evaluation and consult the appropriate
section that follows.
POOR OVERALL SENSITIVITY
Poor overall sensitivity may be caused by a variety of
factors arid is roughly judged by the size of the peak
obtained from 20ng of DFTPP. The operator must be
familiar with the capabilities of the instrument when it
is in good working order. The following list of possible
causes of poor overall sensitivity is ordered from the
first things to check to some actions of nearly last
resort:
1. For packed columns connected to a jet
separator, the mass spectrometer pressure
should be about !0~5 mm of Hg. A lower
pressure suggests f. plugged separator; check
the temperatures of the separator and transfer
line oven for a possible heater failure. A cool
oven will reduce sensitivity by condensation of
the test compound.
2. The dilute standard solution of DFTPP should
be remade if it .is noj fresh. Old solutions of all
dilute standards suffer concentration losses
due to adsorption of trace quantities on the
walls of containers or oxidation by trace
quantities of oxygen or other oxidizing agents.
3. If the shape of the peak is broader than normal
or exhibits tailing, the column may be poorly
conditioned or suffering from old age. Also the
metal fritted filter or separator may be partly
plugged.
4. The tune-up should be checked for over
resolved peaks in any or all mass ranges. Use
only as much resolution as needed as
illustrated in section 2.2. Note carefully the
proper functioning of all tune-up
potentiometers. Recalibrate and repeat the
DFTPP performance evaluatibn.
5. The peak profile diagnostic program should be
run with particular attention to noisy peaks
and possible ground loop problems and other
instabilities as discussed in section 9.4.
6. Clean the ion source, check for a sagging
filament, and clean the rods according to the
manufacturers's procedures.
7. If all else fails, recondition electron multiplier
using procedures from the manufacturer's
manual.
POOR HIGH MASS SENSITIVITY
This condition is revealed by unacceptable ion
abundance at masses 365 and 442 in the DFTPP
spectrum. Poor high mass sensitivity is most frequently
caused by dirty rods or over resolution of masses 219
and 220 and 502 and 503 as in manufacturer's tune-up
procedure. If a tune-up according to the EPA
procedure in section 2.2 is not successful, clean the ion
source and rods.
INCORRECT MASS
ASSIGNMENTS OR POOR
RESOLUTION OF ADJACENT IONS
This condition is revealed by an examination of ion
abundances in the DFTPP spectrum at masses 68-70,
197-199 and 441-443. If the mass scale calibrated
correctly, but incorrect mass assignments appear in the
DFTPP spectrum, a slow drift of the mass scale
calibration is indicated. This is most frequently caused
by a weak 6AL5 tube in the RF generator (1015 and
3000 series instruments). Refer to section 9.4 and locate
the cause of the drift.
If the mass assignments are correct but the ions a:
masses 68, 197, or 441 are too abundant, front end lift
off is indicated. This condition is ofter caused by an
incorrect alignment of the source magnet or incorrect
adjustment of the ion source potentials (lens, extractor,
ion volume, etc.).
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Insufficient resolution will cause excessive ion
abundance at masses 68, 197 or 441 as well as at masses
70, 199, or 443. Acceptable ion abundance at masses
68, 197, or 441, but inaccurate 69/70, 198/199, or
442/443 ratios may be caused by a system zero
adjustment that sets the threshold too high and clips off
real ion abundance data.
HIGH BACKGROUND
High background is defined as the presence of
extraneous ions in an otherwise acceptable spectrum of
20ng of DFTPP. A more or less continuous band of
ions across a broad mass range suggests a poor system
zero adjustment, in which the threshold is set too low.
Repeat the zero adjustment in section 2.4 and make
sure one accumulator light is either just flashing or just
off. If a steady zero cannot be achieved, see section 9.3
for possible causes.
Chemical background can result from a serious
accumulation of pump oil in the manifold, solid probe,
or transfer line flange area. This could be caused by a
lengthy power failure and the resultant diffusion of oil
vapor or by a failure in the overheat protect circuit that
allowed a diffusion pump to overheat. Removal of
pump oil is accomplished by a thorough internal
cleaning of the system with solvents and the
manufacturer should be consulted for assistance.
Chemical background can also result from liquid
phase bleeding from the GC column, contaminated
carrier gas, a contaminated injection system, or a small
leak in the GC column. As appropriate the column
should be operated at a lower temperature,
reconditioned or changed. If this fails to eliminate the
background change or regenerate the carrier gas filter
drying trap or change the carrier gas cylinder. Injector
contamination can be eliminated by a thorough
cleaning of the injection port with a series of solvents.
However, if on-column injection is employed, cleaning
the injection port will not help. If the head of the
column is highly contaminated, discard the old
packing, thoroughly clean the column, and repack.
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CHAPTER 10
SELECTED BIBLIOGRAPHY
It is not the purpose of this chapter to present a
comprehensive listing of all the known literature of
GC/MS 'and related articles on enviriomental
applications. Rather a limited number of books, review
articles, and original journal articles are cited which are
considered important contributions and keys to further
information about these subjects.
10.1 GENERAL REFERENCE BOOKS
S. Safe and O. Hutzinger, "Mass Spectrometry of
Pesticides and Pollutants", CRC Press, Cleveland,
OH, 1973.
R.E. Gould, "Fate of Organic Pesticides in the
Aquatic Environment", Advances in Chemistry
Series No. Ill, American Chemical Society,
Washington, D.C., 1972.
F.W. McLafferty, "Interpretation of Mass Spectra",
2nd ed., W.A. Benjamin, Inc., New York, N.Y.,
1973.
G.W.A. Milne, "Mass Spectrometry, Techniques
and Applications", Interscience Publishers, John
Wiley and Sons, Inc., New York, N.Y., 1971.
H. Budzikiewicz, C. Djerassi, and D.H. Williams,
"Mass Spectrometry of Organic Compounds",
Holden-Day Inc., San Francisco, CA, 1967.
J. Roboz, "Introduction to Mass Sriectrometry,
Instrumentation and Techniques", Interscience
Publishers, John Wiley and Sons, Inc., New York,
N.Y. 1968.
W. McFadden, "Techniques of Combined Gas
Chromatography/Mass Spectrometry-Applications
in Organic Analysis", Interscience Publishers, John
Wiley and Sons, Inc., New York, N.Y.,1973.
G.R. Waller, "Biochemical Applications of Mass
Spectrometry", Interscience Publishers, John Wiley
and Sons, Inc., New York, N.Y., 1971.
Q.N. Porter and J. Baldas, "Mass Spectrometry of
Heterocyclic Compounds", Interscience Publishers,
John Wiley and Sons, Inc., New York, N.Y., 1971.
F.W. McLafferty, "Mass Spectrometry of Organic
Ions", Academic Press, Inc., New York, N.Y., 1963.
J.H. Beynon, R.A. SauhderSi and A.E. Williams,
"The Mass Spectra of Organic Molecules", Elsevier
Publishing Co., New York, N.Y., 1968.
K. Biemann, "Mass Spectrometry-Organic
Chemical Applications", McGraw-Hill Book Co.,
Inc., New York, N.Y., 1962.
M.C. Hamming and N.G. Foster, "Interpretation of
Mass Spectra of Organic Compounds", Academic
Press, New York; N.Y., 1972.
H.M. McNair and E.J. Bonelli, "Basic Gas
Chromatography", Varian Aerograph, Walnut
Creek, CA, 1969.
W.R; Supina, "The Packed Column in Gas
Chromatography", Supelco, Inc., Bellefonte, PA,
1974.
T.R. Lynn, "Guide to Stationary Phases for Gas
Chromatography", Analabs, Inc., North Haven, CT,
1975!
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10.2 PRINTED MASS SPECTRA
COLLECTIONS
A. Cornu and R. Massot, "Compilation of Mass
Spectral Data", 2nd ed., Heyden and Son, Ltd.,
London, England, 1975.
"Eight Peak Index of Mass Spectra", Vol. 1-3, Mass
Spectrometry Data Centre, Atomic Weapons
Research Establishment, AJdermaston, England,
1975
E. Stenhagen, S. Abrahamssen, and F.W.
McLafferty, "Registry of Mass Spectral Data",
Interscience Publishers, John Wiley and Sons, Inc,
New York, NY, 1974.
"EPA/NIH Mass Spectral Data Base", National
Bureau of Standards, National Standard Reference
Data Service publication No. 63 (1978).
10.3 SELECTED REVIEW AND
PRIMARY JOURNAL ARTICLES
MASS SPECTROMETRY
Burlingame, A.L., Shackleton, C.H.L., Howe, I.,
Chizhov, O.S., Anal. Chem. Annual Reviews, 50,
346R(1978).
Burlingame, A.L., Kimble, B.J., and Derrick, P.J.,
Anal. Chem. Annual Reviews, 48,368R (1976).
Burlingame, A.L., Cox, R.E., and Derrick, P.J.,
Anal. Chem. Annual Reviews, 46,248R (1974).
Burlingame, A.L. and Johanson, G.A., Anal. Chem.
Annual Reviews, 44, 337R (1972).
DeJongh, D.C., Anal. Chem. Annual Reviews, 42,
169R(1970).
Large, R. and Knof, H., Org. Mass Spectrom., 11,
582(1975).
Fales, H.M., Milne, G.W.A., Winkler, H.V., Beckey,
H.D., Damico, J.N., and Barron, R., Anal. Chem.,
47(2), 207 (1975).
Alford. A., Biomed. Mass Spectrom., 2, 229 (1975).
Heller, S.R., Milne, G.W.A., and Feldmann, R.J.,
Science, 195,253(1977).
GC/MS
Fenselau, C, Appl. Spectrosc.. 28 (4), 305 (1974).
Brooks, C.J. and Middleditch, B.S., Mass Spectrom.,
2,302(1973).
Junk, G.A., Int. J; Mass Spectrom. Ion Phys., 8(1), 1
(1972).
Oswald, E.O., Albro, P.W., and McKmnery, J.P., L_
Chromatogr., 98(2), 363 (1974).
Heller, S.R., McGuire, J.M., and Budde, W.L.,
Environ. Sci. Technol., 9,210 (1975).
Eichelberger, J.W., Harris, L.E., and Budde, W.L.,
Anal. Chem.. 47,995 (1975).
DIRECT AQUEOUS INJECTION
Harris, L.E., Budde, W.L., and Eichelberger, J.W.,
Anal. Chem., 46, 1912(1974).
"Standard Methods for the Examination of Water
and Wastewater", 13th Edition, 1971.
Baker, R.A., J. Amer. Water Works Ass., 58, 751
(1966).
Fujii, T., J. Chromatogr., 139,297 (1977).
INERT GAS PURGING AND TRAPPING
Bellar, T.A. and Lichtenberg, J.J., J. Amer. Water
Works Ass., 66, 739 (1974).
F.C. Kopfler, R.G. Melton, R.D. Lingg, and W.E.
Coleman in "Identification and Analysis of Organic
Pollutants in Water", 1st ed., L.H. Kieth, Ed., Ann
Arbor Science Publishers Inc., Ann Arbor, MI,
1976. Chapter 6.
139
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Bellar, T.A., Lichtenberg, J.J., and Kroner, R.C., J._
Amer. Water Works Ass.. 66,703 (1974).
"The Analysis of Trihalomethanes in Finished
Waters by the Purge and Trap Method",
Environmental Monitoring and Support Laboratory,
U.S.'JEnvironmental Protection Agency, Cincinnati,
OH, 1977.
Bellar, T.A. and Lichtenberg, J.J., "Semi-
Automated Headspace Analysis of Drinking Waters
and Industrial Waters for Purgeable Volatile
Organic Compounds" submitted for publication to
ASTM, July 1978.
Bellar, T.A., Lichtenberg, J.J. and Eichelberger,
J.W., Environ. Sci. Technol., 10, 9"26 (1976).
ADSORPTION WITH POROUS
POLYMERS
Junk, G.A., Richard, J.J., Grieser, M.D., Witiak, D.,
WTtiak, J.L., Arguello, M.D., Vick, R., Svec, H.J.,
Fritz, J.S., and Calder, G.V., J. Chromatogr., 99, 745
(1974).
R.G.Webb, EPA Report EPA-660/4-75-003,
Athens, GA, June 1975.
G.R. Harvey, EPA Report EPA-R2-73-177,
March, 1973.
Van Rossum, P., and Webb, R.G., J. Chromatogr.,
150,381(1978).
Coleman, W.E., Lingg, R.D., Melton, R.G. and
Kopfler, F.C., in "Identification and Analysis of
Organic Pollutants in Water", L.W. Keith, Ed.,
305-327, Ann Arbor Science, Ann Arbor, Mich.,
1976.
Symons, J.M., Bellar, T.A., Carswell, J:K.,
DeMarco, J., Kropp, K.L., Robeck, G.G., Seeger,
D.R., Slocum, C.J., Smith, B.L. and Stevens, A.A., J._
Amer. Water Works Assoc., 67, 634, (1975).
Brass, H.J., Feige, M.A., Halloran, T., Mello, J.W.,
Munch, D. and Thomas, R.F., in "Drinking Water
Quality Enhancement Through Source Protection",
R.B. Pojasek, Ed., 393-416, Ann Arbor Science,
Ann Arbor, Mich., 1977.
Bellar, T.A. and Lichtenberg, J.J., presented at the
ASTM Symposium on "The Measurement of
Organic Pollutants in Water and Wastewater",
Denver, CO., June, 1978.
AIR SAMPLES
Grob, K., J. Chromatogr., 62, 1 (1971).
Lao, R.C., Thomas, R.S., Oja, H., and Dubois, L.,
Anal. Chem., 45(5), 908 (1973).
Pellizzari, E.D., Bunch, J.E., Berkley, R.E., and
McRae, J., Anal. Chem., 48(6), 803 (1976).
Bunn, W.W., Deane, E.R., Klein, D.W., and
Kleopfer, R.D., Water, Air, and Soil Pollution,. 4,
367(1975).
FATTY TISSUE SAMPLES
Kuehl, D.W. and Leonard, E.N., Anal. Chem. 50,
182(1978).
Bellar, T.A., Budde, W.L. and Eichelberger, J.W. in
"Monitoring Techniques for Toxic Substances" D. CHEMICAL DERIVATIZATION
Schuetzle,, Ed., American Chemical Society, 1978.
QUALITATIVE HEADSPACE ANALYSIS
McAullife, C, Chem. Tech., 46 (1971).
A.E. Pierce, "Silylation of Organic Compounds",
Pierce Chemical Co., Rockford, IL, 1968.
K. Blau and G. King, "The Handbook of
Derivatives for Chromatography", Heyden and Son,
Ltd., New York, NY, 1977.
140
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SELECTED ION MONITORING
Bu'dde. W.L.. . and Eichelberger. J.W., I_
C):rornaiOgr., 1J4. 147(1977).
Hichs!b.er»er, J.W., Harris, L.E., and Budde, W.L.,
Anal. Chem., 46, 227 (1974).
OPEN TUBULAS COLUMNS
Grab, K., Anal. Chem.. 45,1783(1973).
Grab, K. and Grob K. Jr., J. Chrotnatogr., 94, 53
(1974).
Novotny, M., Anal. Chem.. 50,16A (1978).
CHEMICAL IONIZATION
Jelus, B.L. and Munson, B., Biomed. Mass
Spectrom.. 1,96(1974).
Hatch, F. and Munson, B., Anal. Chem. 49(1), 169
(1977).
Field, F.H., Advnn. Mass Spectrom.. 4, 645 (1953).
Munson, B.. Anal. Cheni., 49, 772A (1977).
Hunt, D.F., StatTord, G.C., Crow, F.W., and
Russell, J.W., Anal. Cherr... 48 (14), 2098 (1976).
Price, P., Martinsen, D.P., Upham, R.A., SwotTord,
H.S., and Buttrill, S.E., Anal. Chem., 47 (1), 190
(1975).
Murata, T., Takahashi, 7., and Takcda, T., Anal.
Chem. 47 (3), 573 (1975).
Oswald, E.O., Levy, L.. Corbett, B.J. and Walker,
M.P..J. Chromatogr., 93, 63 (1974).
Fales, H.M., Milne, G.W.A., and Nicholson, R.S.,
Anal. Chem., 43 (13), 1785 (1971).
Holmstead, R.L. and Casida, J.E., J. Ass. Offlc.
Anal. Chem., 57(5), 1050(1974).
Biros, F.J., Dougherty, R.C., and Dalton, J., Org.
Mass Spectrom.. 6(11), 1161(1972).
141
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