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