maxquant step by step rs091124
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UsingMaxQuantforproteomicsAstepbystepguide
RongxiaoSa,DepartmentofChemistry
Pra@kJagtap,MinnesotaSupercompu@ngIns@tuteNov24,2009
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Outline
StepbystepprocedureonusingMaxQuantforproteiniden@ca@on(salivaproteins,6rawles)
RawdataprocessingMascotsearchingproteingroupingandlegenera@ng
BriefprocedureonusingMaxQuantforSILACdata
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WhychooseMaxQuant
Freeanduserfriendly,greatusersupportfromdiscussiongroup
Fasterthanotheralgorithms
Greatforlargedatasets(>5G)
Moreproteiniden@ca@on,ormoreMS/MSiden@ed
Crossreferencetovariousdatabases(GO,Swissprot,Ensembl,KEGG)
GreatforSILACquan@ca@on
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SystemrequirementsforrunningMaxQuant
WindowsXPorvista32bitopera@ngsystem
Xcaliburinstalledonthesamecomputer
MascotDaemoninstalledoraccess
Atleastdualcoreprocessor(or2Duo)
Atleast2GRAM
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Correctdataacquisi@onmodeonLTQorbitrap
MSscanshouldbeacquiredinprolemode,MS/MScentroidmode
Uselockmasscalibra@on
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Login
Eitheronsdvlapp32oronpc1,pc2,pc3inWalterlibrary585withyouruseraccount
DoubleclickontheMaxQuantfoldershortcutonthedesktop
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Tutorialleloca@on
Mycomputer\C:\Documentandsecngs\allusers\sharedtutorial
Foryourownpurposes,putyourlesinUdrive
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Acknowledgements
EricSanfordinMSI
MadStoneinBMBB
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Astepbystepguide
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Loginview
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Proteinandpep@degrouping,quan@ca@on
GenerateMSMlesformascotsearching
Generatedecoydatabases
ModulesofMaxQuant
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Quant.exe
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LoadingrawlesC:\Documentsandsecngs\allusers\shareddocuments\proteomicworkshop\rawles
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Selectnumberofthreads=2
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SelectParameters
SelectSingletsfornonlabeleddataSelectDoubletsforSILACdatawith2experimentsSelecttripletsforSILACdatawith3experiments
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SelecthIPI_Maxquantfordatabaseforhumansamples
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Selecttrypsinforenzyme
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Star@ngQuant.exe
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Processedlesarelocatedinthesamefolderasrawlesareandareinthefoldernamedcombined
Quant.exeDone
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Quant.exegeneratedles
C:\documentsandsecngs\allusers\shareddocuments\proteomicsworkshop\rawles\combined
Allspectra.CID.iso.parAllspectra.CID.iso_0.msmAllspectra.CID.sil0.parAllspectra.CID.sil0_0.msmAllspectra.CID.sil1.parAllspectra.CID.sil1_0.msm
Mascotparameterles CorrespondingMSMles
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Mascotdatabasesearching
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SelectsearchparametersParameterleloca@on:C:\documentsandsecngs\allusers\shareddocuments\proteomicstutorial\processedles
Cau@on:Parameterlescannotbeonnetdrive(Udrive),ithastobesavedonC:orEdriveonSdvlapp32,pc1,pc2andpc3
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Selecttaskeditorparameters
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SelectMSMleforsearching
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SearchFinished
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FileLoca@on
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Datledownload
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Datledownload
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Proteingroupingwithiden@fy.exe
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Uploadrawles
Rawlesloca@on:C:\DocumentsandSecngs\allusers\shareddocuments\Proteomicsworkshop\Rawles
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UploadDatles
Datlesloca@on:C:\DocumentsandSecngs\allusers\shareddocuments\Proteomicsworkshop\datles
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UploadProteinDatabase
ProteinDatabaseloca@on:C:\DocumentsandSecngs\allusers\shareddocuments\Proteomicsworkshop\databases
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UploadExperimentaldesignle
ProteinDatabaseloca@on:C:\DocumentsandSecngs\allusers\shareddocuments\Proteomicsworkshop\Processedles\combined
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Changingparametersforproteinpep@degrouping
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Proteinandpep@degroupinginprocess
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Proteinandpep@degrouplesloca@on
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Proteinandpep@degrouples
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