U.S. Department of Commerce

　　Technology Administration

　　National Institute of Standards and Technology (NIST)

　　Standard Reference Data Program

　　Gaithersburg, MD 20899

　　The National Institute of Standards and Technology (NIST) uses its best efforts to deliver a high quality copy of the database and the associated software and to verify that the data contained therein have been selected on the basis of sound scientific judgment and that the software is functioning correctly. However, NIST makes no warranties to that effect and NIST shall not be liable for any damage that may result from errors or omissions in the database or its associated software.

　　Copyright 1977, 1978, 1980, 1982, 1987, 1988, 1990, 1992, 1997, 2000, 2004 copyright by the U.S. Secretary of Commerce on behalf of the United States of America. All rights reserved. No part of this database may be reproduced, stored in a retrieval system, or transmitted, in any form. or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the Standard Reference Data Program at NIST.

　　Table of Contents

　　AMDIS — USER GUIDE. i

　　1 Introduction. 1

　　1.1 The AMDIS Program.. 1

　　1.2 How to Use This User Guide. 1

　　1.3 Conventions Used in This User Guide. 2

　　1.4 An Overview of Automated GC/MS Identification by Steve Stein. 2

　　1.4.1 Background. 2

　　1.4.2 Previous Work. 3

　　1.4.3 Method. 3

　　1.4.4 References. 3

　　2 Getting Started. 5

　　2.1 Introduction. 5

　　2.2 Simultaneously Viewing AMDIS and its Help Window.. 5

　　2.3 Getting AMDIS into a Known State. 5

　　2.4 Confirm Window and Results Window Overview.. 6

　　2.5 Confirm Window Appearance. 6

　　2.5.1 Chromatogram Display. 9

　　2.5.2 Profile Display. 9

　　2.5.3 Information Lists. 10

　　2.5.4 Mass Spectral Display. 10

　　2.5.5 Changing the Display Range. 11

　　2.6 Results Window Appearance. 11

　　2.6.1 Control Panel 12

　　2.6.2 Information Lists. 12

　　2.6.3 Information Tabs. 13

　　2.7 Analysis Modes Overview.. 13

　　2.8 Analysis Mode - Simple. 13

　　2.8.1 Searching the NIST Database. 17

　　2.9 Analysis Mode - RI Calibration/Performance. 17

　　2.10 Analysis Mode - Use RI Calibration Data. 21

　　2.11 Analysis Mode - Use Internal Standards. 25

　　2.12 Analysis Mode - Use RI Calibr. Data + Internal Std. 28

　　2.13 Analysis Mode - Performance Check. 31

　　2.14 Recap. 35

　　3 AMDIS Confirm Window.. 36

　　3.1 Introduction. 36

　　3.2 Menu Bar 37

　　3.2.1 File Menu. 38

　　3.2.2 Analyze Menu. 45

　　3.2.3 Mode Menu. 54

　　3.2.4 View Menu. 55

　　3.2.5 Library Menu. 58

　　3.2.6 Options Menu. 59

　　3.2.7 Window Menu. 63

　　3.2.8 Help Menu. 64

　　3.3 Button Bar 64

　　3.3.1 Run. 64

　　3.3.2 Rescale. 64

　　3.3.3 Info. 65

　　3.3.4 Arrowheads. 65

　　3.3.5 Manual-On and Manual-Off 65

　　3.3.6 Deconv. 65

　　3.4 Data Displays. 65

　　3.4.1 Chromatogram Display. 66

　　3.4.2 Profile Display. 72

　　3.4.3 Information Lists. 74

　　3.4.4 Mass Spectral Display. 81

　　3.5 Display of Multiple Chromatograms. 88

　　3.5.1 Multiple Chromatograms in Independent Windows. 88

　　3.5.2 Two Chromatograms in One Window.. 89

　　4 AMDIS Results Window.. 90

　　4.1 Introduction. 90

　　4.2 Control Panel 91

　　4.2.1 Analyze. 92

　　4.2.2 Help. 92

　　4.2.3 Done. 92

　　4.2.4 Confirm.. 92

　　4.2.5 Print 93

　　4.2.6 Load Results. 93

　　4.3 Information Lists. 93

　　4.4 Information Tabs. 94

　　5 Auxiliary Information. 95

　　5.1 Introduction. 95

　　5.2 Library Tab. 96

　　5.3 Spectra Tab. 96

　　5.4 Settings Tab. 97

　　5.5 Standards Tab. 97

　　5.5.1 External Standard Mode. 97

　　5.5.2 Internal Standard Mode. 98

　　5.6 QA/QC Tab. 98

　　5.6.1 Results. 99

　　5.6.2 Performance. 100

　　5.7 S/N Tab. 101

　　5.7.1 Signal 101

　　5.7.2 Noise. 101

　　5.8 Options Tab. 102

　　6 Analysis. 103

　　6.1 Introduction. 103

　　6.2 Analysis Types. 103

　　6.2.1 Simple. 104

　　6.2.2 RI Calibration/Performance. 105

　　6.2.3 Use RI Calibration Data. 105

　　6.2.4 Use Internal Standards. 107

　　6.2.5 Use RI Calibr. Data + Internal Standards. 108

　　6.2.6 Performance Check. 109

　　6.3 Library Types. 110

　　6.4 Analysis Settings. 111

　　6.4.1 Identif. (Identification) Tab) 111

　　6.4.2 Instrument Tab. 113

　　6.4.3 Deconv. (Deconvolution) Tab. 114

　　6.4.4 Libraries. 115

　　6.4.5 Quality Control (QA/QC Tab) 115

　　6.4.6 A Note on RI Calibration/Performance Analysis. 116

　　7 Post Analysis Classification of Spectra. 117

　　7.1 Postprocess. 117

　　7.2 Structural Classifiers. 117

　　7.3 CW Classifier (Chemical Weapons Related Classifiers) 117

　　7.4 Spectral Similarity. 117

　　7.5 Compare Data Files. 117

　　7.6 Varmuza Classification References. 118

　　8 Library Development and Maintenance. 119

　　8.1 Introduction to Libraries. 119

　　8.2 Library Types. 119

　　8.3 Library Editors. 120

　　8.3.1 Build One Library. 120

　　8.3.2 Library Transfer 120

　　8.4 Library Window Functions. 121

　　8.4.1 Library Information and Display Options. 121

　　8.4.2 Editing Options. 121

　　8.4.3 Other Options. 121

　　8.5 Compound and Spectra Editors. 122

　　8.5.1 Compound Information Editor 122

　　8.5.2 Spectrum Editor 123

　　8.6 Setting up Calibration Files for Use with AMDIS. 124

　　8.6.1 Create Calibration Library from a Data File. 124

　　8.6.2 Create Library from NIST MS Database. 125

　　8.7 Using the Performance Log Feature. 125

　　8.8 Viewing the Library or Calibration. 126

　　8.9 Format of Mass Spectral Transfer (MSP) Files. 126

　　9 Batch Jobs. 128

　　9.1 Create and Run Job. 128

　　9.2 Show Results of Last Job. 128

　　10 Manual Deconvolution. 129

　　10.1 Overview of Manual Deconvolution. 129

　　10.2 Background Subtraction. 129

　　10.3 Manual Deconvolution. 130

　　11 How Do I … ?. 131

　　11.1 System Setup. 131

　　11.1.1 How Do I Change the Settings for An Analysis?. 131

　　11.1.2 How Do I Find Out What Settings Were Used for the Current Analysis?. 131

　　11.2 Data Analysis. 131

　　11.2.1 Analysis Without Retention Index Data (Simple Analysis) 131

　　11.2.2 Analysis With Retention Index Data. 131

　　11.2.3 How Do I Examine an Old Analysis?. 131

　　11.2.4 How Do I Use Data for Calibration and Performance Monitoring. 132

　　11.2.5 How Do I Search the NIST Database with a Component?. 132

　　11.3 Library Maintenance. 132

　　11.3.1 How Do I Add Spectra to a Library?. 132

　　11.3.2 How Do I Delete Spectra From a Library?. 132

　　11.3.3 How Do I Edit Spectra or Compound Information in a Library?. 132

　　11.4 Display Modification. 133

　　11.4.1 How Do I Expand (Zoom) a Plot?. 133

　　11.4.2 How Do I Switch Between Log and Linear Axis?. 133

　　11.4.3 How Do I Change Colors and Weight of Lines?. 133

　　11.4.4 How Do I Find the Exact Position of a Peak?. 133

　　11.4.5 How Do I Show Components on a Plot?. 133

　　11.4.6 How Do I Change the Data that is Shown or Printed About a Component?. 133

　　12 Varmuza Compound Classification Analysis. 134

　　13 Glossary. 144

　　14 File Formats. 145

　　14.1 CAL File. 145

　　14.2 Report File. 145

　　15 Contacts. 146

　　15.1 Technical 146

　　15.2 Business. 146