UsingMaxQuantforproteomics

Astepbystepguide

RongxiaoSa,DepartmentofChemistry
Pra@kJagtap,MinnesotaSupercompu@ngIns@tute
Nov24,2009

Outline
StepbystepprocedureonusingMaxQuantfor
proteiniden@ca@on(salivaproteins,6rawles)
RawdataprocessingMascotsearchingprotein
groupingandlegenera@ng
BriefprocedureonusingMaxQuantforSILACdata

WhychooseMaxQuant
Freeanduserfriendly,greatusersupportfromdiscussion
group
Fasterthanotheralgorithms
Greatforlargedatasets(>5G)
Moreproteiniden@ca@on,ormoreMS/MSiden@ed
Crossreferencetovariousdatabases(GO,Swissprot,
Ensembl,KEGG)
GreatforSILACquan@ca@on

Systemrequirementsforrunning
MaxQuant
WindowsXPorvista32bitopera@ngsystem
Xcaliburinstalledonthesamecomputer
MascotDaemoninstalledoraccess
Atleastdualcoreprocessor(or2Duo)
Atleast2GRAM

Correctdataacquisi@onmodeonLTQ
orbitrap
MSscanshouldbeacquiredinprolemode,
MS/MScentroidmode
Uselockmasscalibra@on

Login
Eitheronsdvlapp32oronpc1,pc2,pc3inWalter
library585withyouruseraccount
DoubleclickontheMaxQuantfoldershortcutonthe
desktop

Tutorialleloca@on

Mycomputer\C:\Documentandsecngs\allusers\sharedtutorial
Foryourownpurposes,putyourlesinUdrive

Acknowledgements
EricSanfordinMSI
MadStoneinBMBB

Astepbystepguide

Loginview

ModulesofMaxQuant

Proteinandpep@degrouping,quan@ca@on
GenerateMSMlesformascotsearching
Generatedecoydatabases

Quant.exe

Loadingrawles
C:\Documentsandsecngs\allusers\shareddocuments\proteomicworkshop
\rawles

Selectnumberofthreads=2

SelectSingletsfornonlabeleddata
SelectDoubletsforSILACdatawith2experiments
SelecttripletsforSILACdatawith3experiments

SelectParameters

SelecthIPI_Maxquantfordatabase
forhumansamples

Selecttrypsinforenzyme

Star@ngQuant.exe

Quant.exeDone

Processedlesarelocatedinthesamefolderasrawlesareandareinthefoldernamed
combined

Quant.exegeneratedles
C:\documentsandsecngs\allusers\shareddocuments\proteomicsworkshop\rawles
\combined

Mascotparameterles

CorrespondingMSMles
Allspectra.CID.iso.parAllspectra.CID.iso_0.msm
Allspectra.CID.sil0.parAllspectra.CID.sil0_0.msm
Allspectra.CID.sil1.parAllspectra.CID.sil1_0.msm

Mascotdatabasesearching

Selectsearchparameters
Parameterleloca@on:C:\documentsandsecngs\allusers\shareddocuments\
proteomicstutorial\processedles

Cau@on:Parameterlescannotbeonnetdrive(Udrive),ithastobesavedonC:orEdriveon
Sdvlapp32,pc1,pc2andpc3

Selecttaskeditorparameters

SelectMSMleforsearching

SearchFinished

FileLoca@on

Datledownload

Datledownload

Proteingroupingwithiden@fy.exe

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