AMDIS操作说明资料

File:

FILENAME\*FirstCap

AMDIS-Manual.doc

Date:

SAVEDATE\@"dMMMM,yyyy"

12November,2004

Page

AMDIS—USERGUIDE

PeterD’ArcyandW.GaryMallard

Automated

MassSpectral

Deconvolution&

Identification

System

U.S.DepartmentofCommerce

TechnologyAdministration

NationalInstituteofStandardsandTechnology(NIST)

StandardReferenceDataProgram

Gaithersburg,MD20899

TheNationalInstituteofStandardsandTechnology(NIST)usesitsbesteffortstodeliverahighqualitycopyofthedatabaseandtheassociatedsoftwareandtoverifythatthedatacontainedthereinhavebeenselectedonthebasisofsoundscientificjudgmentandthatthesoftwareisfunctioningcorrectly.However,NISTmakesnowarrantiestothateffectandNISTshallnotbeliableforanydamagethatmayresultfromerrorsoromissionsinthedatabaseoritsassociatedsoftware.

Copyright1977,1978,1980,1982,1987,1988,1990,1992,1997,2000,2004copyrightbytheU.S.SecretaryofCommerceonbehalfoftheUnitedStatesofAmerica.Allrightsreserved.Nopartofthisdatabasemaybereproduced,storedinaretrievalsystem,ortransmitted,inanyformorbyanymeans,electronic,mechanical,photocopying,recording,orotherwise,withoutthepriorwrittenpermissionoftheStandardReferenceDataProgramatNIST.

Page

File:

FILENAME\*FirstCap

AMDIS-Manual.doc

Date:

SAVEDATE\@"dMMMM,yyyy"

12November,2004

Page

TableofContents

AMDIS—USERGUIDE

i

1 Introduction

1

1.1 TheAMDISProgram

1

1.2 HowtoUseThisUserGuide

1

1.3 ConventionsUsedinThisUserGuide

2

1.4 AnOverviewofAutomatedGC/MSIdentificationbySteveStein

2

1.4.1 Background

2

1.4.2 PreviousWork

3

1.4.3 Method

3

1.4.4 References

3

2 GettingStarted

5

2.1 Introduction

5

2.2 SimultaneouslyViewingAMDISanditsHelpWindow

5

2.3 GettingAMDISintoaKnownState

5

2.4 ConfirmWindowandResultsWindowOverview

6

2.5 ConfirmWindowAppearance

6

2.5.1 ChromatogramDisplay

9

2.5.2 ProfileDisplay

9

2.5.3 InformationLists

10

2.5.4 MassSpectralDisplay

10

2.5.5 ChangingtheDisplayRange

11

2.6 ResultsWindowAppearance

11

2.6.1 ControlPanel

12

2.6.2 InformationLists

12

2.6.3 InformationTabs

13

2.7 AnalysisModesOverview

13

2.8 AnalysisMode-Simple

13

2.8.1 SearchingtheNISTDatabase

17

2.9 AnalysisMode-RICalibration/Performance

17

2.10 AnalysisMode-UseRICalibrationData

21

2.11 AnalysisMode-UseInternalStandards

25

2.12 AnalysisMode-UseRICalibr.Data+InternalStd.

28

2.13 AnalysisMode-PerformanceCheck

31

2.14 Recap

35

3 AMDISConfirmWindow

36

3.1 Introduction

36

3.2 MenuBar

37

3.2.1 FileMenu

38

3.2.2 AnalyzeMenu

45

3.2.3 ModeMenu

54

3.2.4 ViewMenu

55

3.2.5 LibraryMenu

58

3.2.6 OptionsMenu

59

3.2.7 WindowMenu

63

3.2.8 HelpMenu

64

3.3 ButtonBar

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-OnandManual-Off

65

3.3.6 Deconv

65

3.4 DataDisplays

65

3.4.1 ChromatogramDisplay

66

3.4.2 ProfileDisplay

72

3.4.3 InformationLists

74

3.4.4 MassSpectralDisplay

81

3.5 DisplayofMultipleChromatograms

88

3.5.1 MultipleChromatogramsinIndependentWindows

88

3.5.2 TwoChromatogramsinOneWindow

89

4 AMDISResultsWindow

90

4.1 Introduction

90

4.2 ControlPanel

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 LoadResults

93

4.3 InformationLists

93

4.4 InformationTabs

94

5 AuxiliaryInformation

95

5.1 Introduction

95

5.2 LibraryTab

96

5.3 SpectraTab

96

5.4 SettingsTab

97

5.5 StandardsTab

97

5.5.1 ExternalStandardMode

97

5.5.2 InternalStandardMode

98

5.6 QA/QCTab

98

5.6.1 Results

99

5.6.2 Performance

100

5.7 S/NTab

101

5.7.1 Signal

101

5.7.2 Noise

101

5.8 OptionsTab

102

6 Analysis

103

6.1 Introduction

103

6.2 AnalysisTypes

103

6.2.1 Simple

104

6.2.2 RICalibration/Performance

105

6.2.3 UseRICalibrationData

105

6.2.4 UseInternalStandards

107

6.2.5 UseRICalibr.Data+InternalStandards

108

6.2.6 PerformanceCheck

109

6.3 LibraryTypes

110

6.4 AnalysisSettings

111

6.4.1 Identif.(Identification)Tab)

111

6.4.2 InstrumentTab

113

6.4.3 Deconv.(Deconvolution)Tab

114

6.4.4 Libraries

115

6.4.5 QualityControl(QA/QCTab)

115

6.4.6 ANoteonRICalibration/PerformanceAnalysis

116

7 PostAnalysisClassificationofSpectra

117

7.1 Postprocess

117

7.2 StructuralClassifiers

117

7.3 CWClassifier(ChemicalWeaponsRelatedClassifiers)

117

7.4 SpectralSimilarity

117

7.5 CompareDataFiles

117

7.6 VarmuzaClassificationReferences

118

8 LibraryDevelopmentandMaintenance

119

8.1 IntroductiontoLibraries

119

8.2 LibraryTypes

119

8.3 LibraryEditors

120

8.3.1 BuildOneLibrary

120

8.3.2 LibraryTransfer

120

8.4 LibraryWindowFunctions

121

8.4.1 LibraryInformationandDisplayOptions

121

8.4.2 EditingOptions

121

8.4.3 OtherOptions

121

8.5 CompoundandSpectraEditors

122

8.5.1 CompoundInformationEditor

122

8.5.2 SpectrumEditor

123

8.6 SettingupCalibrationFilesforUsewithAMDIS

124

8.6.1 CreateCalibrationLibraryfromaDataFile

124

8.6.2 CreateLibraryfromNISTMSDatabase

125

8.7 UsingthePerformanceLogFeature

125

8.8 ViewingtheLibraryorCalibration

126

8.9 FormatofMassSpectralTransfer(MSP)Files

126

9 BatchJobs

128

9.1 CreateandRunJob

128

9.2 ShowResultsofLastJob

128

10 ManualDeconvolution

129

10.1 OverviewofManualDeconvolution

129

10.2 BackgroundSubtraction

129

10.3 ManualDeconvolution

130

11 HowDoI…?

131

11.1 SystemSetup

131

11.1.1 HowDoIChangetheSettingsforAnAnalysis?

131

11.1.2 HowDoIFindOutWhatSettingsWereUsedfortheCurrentAnalysis?

131

11.2 DataAnalysis

131

11.2.1 AnalysisWithoutRetentionIndexData(SimpleAnalysis)

131

11.2.2 AnalysisWithRetentionIndexData

131

11.2.3 HowDoIExamineanOldAnalysis?

131

11.2.4 HowDoIUseDataforCalibrationandPerformanceMonitoring

132

11.2.5 HowDoISearchtheNISTDatabasewithaComponent?

132

11.3 LibraryMaintenance

132

11.3.1 HowDoIAddSpectratoaLibrary?

132

11.3.2 HowDoIDeleteSpectraFromaLibrary?

132

11.3.3 HowDoIEditSpectraorCompoundInformationinaLibrary?

132

11.4 DisplayModification

133

11.4.1 HowDoIExpand(Zoom)aPlot?

133

11.4.2 HowDoISwitchBetweenLogandLinearAxis?

133

11.4.3 HowDoIChangeColorsandWeightofLines?

133

11.4.4 HowDoIFindtheExactPositionofaPeak?

133

11.4.5 HowDoIShowComponentsonaPlot?

133

11.4.6 HowDoIChangetheDatathatisShownorPrintedAboutaComponent?

133

12 VarmuzaCompoundClassificationAnalysis

134

13 Glossary

144

14 FileFormats

145

14.1 CALFile

145

14.2 ReportFile

145

15 Contacts

146

15.1 Technical

146

15.2 Business

146

Introduction

TheAMDISProgram

TheAutomaticMassSpectralDeconvolutionandIdentificationSystem(AMDIS)allowsyoutoautomaticallyfindanyofasetoftargetcompoundsinagaschromatography/massspectral(GC/MS)datafile.TheprogramfirstdeconvolutestheGC/MSdatafiletofindalloftheseparatecomponents.Eachofthesecomponentsisthencomparedagainstalibraryoftargetcompounds.Thematchfactorbetweenthetargetspectrumandthedeconvolutedcomponentspectrumisthenreported,ifitisaboveausersetvalue.

AMDISusesalibraryofmassspectrawithorwithoutretentionindicestoidentifycompoundsinthedatafile.Theprogramcanbeconfiguredtobuildaretentionindexcalibrationfile,tousetheretentionindexdataalongwiththemassspectraldataortoworkwithoutreferencetoanyretentionindexdata.Inaddition,AMDIScanbeusedtobuildauserdefinedlibrary,eitherfromGC/MSdatafiles,orfromthedataintheNISTMassSpectralDatabase.

Theprogramwilloptionallytracktheresultsofroutineperformancemixtureruns(suchasthe

xe"Grobtestmixture"

Grobtestmixture).Dataisretainedfrompreviousrunssothatchangesintheperformanceofthesystemcanbemonitored.

AMDISalsoprovidescompoundclassidentification,abatchprocessingcapabilityandaconvenientlinktotheNISTMassSpectralDatabase.

HowtoUseThisUserGuide

Youshouldreadthissectionandthefollowingsection;whichdescribesthetypographicandrelatedconventionsusedinthismanual(

REF_Ref42959267\r\h

1.3

REF_Ref52026657\h

ConventionsUsedinThisUserGuide

).

Itisuseful,althoughnotessential,tounderstandalittleofthebackgroundandmethodologyofAMDISandthatcanbefoundin

REF_Ref49181709\r\h

1.4

REF_Ref49181726\h

AnOverviewofAutomatedGC/MSIdentificationbySteveStein

.

Chapter

REF_Ref49181939\r\h

2

REF_Ref49181960\h

GettingStarted

isessentialreading.ItfirstintroducesyoutothebasicvisualsandafewessentialfeaturesofthetwodifferentuserinterfacesthatAMDISoffers.

Therestofthechapteristhenwrittenintutorialstyleandleadsyouone-by-onethroughallofthe“analysismodes”thatAMDISsupports.Manyusefultopicsareintroducedwhilstdoingthisandtherearemanyreferencestotheircorrespondingdetailedsectionsforthosereaderswhowanttoimmediatelylearnalittlemoreaboutaspecifictopic.

Evenifyoudon’tnormallyreadmanuals,the30minutesorsorequiredtogothroughthischapterwilldramaticallyimproveyourabilitytoquicklystartproductiveworkwithAMDIS.

ItisveryhighlyrecommendedthatyoureadChapter

REF_Ref49183062\r\h

2

.

Thechaptersthatfollowthetutorialsarewritteninthestyleofatechnicalreferenceandaretopic-based,ratherthantutorial-based.TheyprovidefulldetailsofallAMDISparametersandfunctionality.

Chapter

REF_Ref86203122\w\h

11

isalistoffrequentlyaskedquestions(FAQs).Aswellasgivinganswerstoquestions,someusefultipsarealsointroduced.ItmaybeworthyourwhiletoreadthroughthesebeforefinallystartingproductiveworkwithAMDIS.

Chapter

REF_Ref86203123\w\h

12

liststheVarmuzaclassifiers,whoseuseisdescribedin

REF_Ref441474270\w\h

7.2

REF_Ref86679054\h

StructuralClassifiers

.

AlmosteverywhereinAMDIStherightmousebuttonwillbringup“options”(alistofoneormorecommands).Theseoptionswillvaryasyoumovearoundthescreen(theyare“context-sensitive”).Inaddition,theoptionspresentedcanchangeasyouprogressthroughananalysis.

Note: Anoptionthatis“grayedout”(disabled)earlyoninananalysismaybeavailablelater.

ConventionsUsedinThisUserGuide

Commandsthatcanbeselectedfrommenusareinbold.Forexample:ontheViewmenuclickUndock.Sub-menucommandsmayalsobeidentifiedfromahigherlevelmenubyspecifyingthetwoormoremenuitemsseparatedby|.Forexample:clickView|Undock;clickView|ShowMousePosition|OnTop.

Buttonandtabnamesarealsoinbold.Forexample:ToexitfromthedialogclickClose;theStandardstabgivesinformationaboutthestandardsused.

Occasionallyunderlinewillbeusedtohighlightimportantinformation.

Windowanddialognames,pluscertainspecificnamedareasofthedisplay,aregiveninitalics.Forexample:NotetheinformationpresentedintheResultswindow;theAnalysisSettingsdialoghas5tabs;theInformationListsareacanbeundockedandmoved.

Referencestothenames(butnottheselection)ofmodesofanalysiswillappearinitalics.Forexample:ASimpleanalysisdoesnotinvolvetheuseofinternalstandards,buttheUseRICalibr.Data+InternalStd.modedoes.

Referencestosectionsinthismanualarepresentedinnormalfontasasectionnumber,followedbythetitle.Forexample:Theconventionsusedinthisuserguidearedescribedin

REF_Ref42959267\w\h

1.3

REF_Ref52026657\h

ConventionsUsedinThisUserGuide

.Occasionallyasectionreferencemayjustuseitssectionnumber;especiallyifitisbeingrepeatedclosetoitsfirstdefinition.

Referencestocomputerfiles,folders,documentsormanualsaregiveninitalics.Forexample:RefertotheREADME.TXTfile;Readchapter1ofMicrosoft’sIntroductiontoWindowsXPbook.

Namesofcheckboxes,radiobuttonsandotherparameters,valuestobeselectedfromalist,specificvaluesortextshownonthedisplay,texttobeenteredbytypingandwarningmessagesarewritteninboldTimesNewRomanfont.Forexample:ForTypeofanalysis,clickUseInternalStandards;AfterprocessingTotalSignalshowsavalueof1.80e+008;ForFilenametypeNISTEPAoranothernameofyourchoice;AninvalidfileproducestheCannotreadGC/MSdatafilewarningmessage.

Sometimesduringthetutorialsections,itisnecessarytorefertothefolderinwhichAMDISisinstalled.SincethedefaultfoldernameisAMDIS32,thiswillbeused,but,ifyouhaveAMDISinstalledinadifferentfolder,pleasesubstitutethatnamewheneveryouseeAMDIS32mentioned.

AnOverviewofAutomatedGC/MSIdentificationbySteveStein

Background

Gaschromatography/massspectrometry,GC/MS,haslongbeenthemethodofchoiceforidentifyingvolatilecompoundsincomplexmixtures.Thismethodcanfail,however,whenacquiredspectraare“contaminated”withextraneousmassspectralpeaks,ascommonlyarisefromco-elutingcompoundsandionizationchambercontaminants.Theseextraneouspeakscanposeaseriousproblemforautomatedidentificationmethodswheretheycancauseidentificationstobemissedbyreducingthespectrumcomparisonfactorbelowsomepre-setidentificationthreshold.Inaddition,thepresenceofspuriouspeaksinaspectrumaddstotheriskofmakingfalseidentifications.Perhapsworstofall,theaddeduncertaintyleadstoagenerallossofconfidenceinthereliabilityofmakingidentificationsbyGC/MS,especiallyfortracecomponentsincomplexmixtures,akeyapplicationareaforthistechnique.

Themostcommonmethodforextracting“pure”spectraforachromatographiccomponentfromacquiredspectraistosubtractspectrainaselected“background”regionofthechromatogramfromspectraatthecomponentmaximum.This,however,isonlyappropriatewhenbackgroundsignallevelsarerelativelyconstant(ionizationchambercontamination,forexample).Moreover,highlycomplexchromatogramsmayhavenoidentifiable“background”region.

Anautomatedapproachfordealingwithcontaminatedspectraistoassumethatacquiredmassspectralpeaksthatdonotmatchareferencespectrumoriginatefromimpurities.Whilethismethodcanidentifytracecomponentsembeddedincomplexbackgroundspectra,itcanalsoproducefalsepositiveidentificationsfortargetcompoundshavingsimplespectra(i.e.,whentargetcompoundshavespectrawhichare,ineffect,embeddedinthespectraofothercompoundsintheanalyzedmixture).

AMDISisanintegratedsetofproceduresforfirstextractingpurecomponentspectraandrelatedinformationfromcomplexchromatogramsandthenusingthisinformationtodeterminewhetherthecomponentcanbeidentifiedasoneofthecompoundsrepresentedinareferencelibrary.ThepracticalgoalistoreducetheeffortinvolvedinidentifyingcompoundsbyGC/MSwhilemaintainingthehighlevelofreliabilityassociatedwithtraditionalanalysis.

PreviousWork

SincetheinceptionofGC/MS,therehasbeenacontinuinginterestinextracting“pure”componentspectrafromcomplexchromatograms.BillerandBiemann[1]devisedasimplemethodinwhichtheextractedspectrumiscomposedofallmassspectralpeaksthatmaximizesimultaneously.Colby[2]improvedtheresolutionofthismethodbycomputingmorepreciseionmaximizationtimes.Herron,DonnellyandSovocol[3]demonstratedtheutilityofColby’smethodintheanalysisofenvironmentalsamples.

Anothercomputationallyfacileapproachforextractingspectrabasedonsubtractionofadjacentscans(“backfolding”)hasbeenrecentlyproposed[4].Anadvantageofthisapproachisthatitdoesnotexplicitlyrequiremaximization.

AmorecomputationallyintensiveapproachdevelopedbyDromeyetal[5],calledthe“modelpeak”method,extractsionprofilesthathavesimilarshapes.AsintheBiller/Biemannprocedure,thismethodusesmaximainionchromatogramstodetectchromatographiccomponents.Theshapeofthemostprominentofthesemaximizingionchromatogramsisusedtorepresenttheshapeoftheactualchromatographiccomponent.Ionchromatogramswiththisshapeareextractedbyasimpleleast-squaresprocedure.Thismethodwassuccessfullyusedfortargetcompoundidentificationinalarge-scaleEPAstudy[6].Rosenthal[7]proposedanimprovementtothepeakperceptionlogicforthismethod.

Anumberofmatrix-basedapproacheshavebeenproposedthatmakenoassumptionsconcerningcomponentpeakshape.Thesemethodsgenerallyprocessanabundancedatamatrixconsistingofm/z,elutiontimepairs.Setsofionswhoseabundancesarecorrelatedwitheachanotherareextrac