software platforms for quantitative proteomics — dagstuhl seminar —

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1、Softwareplatformsforquantitativeproteomics—DagstuhlSeminar—OleSchulz-TrieglaffInternationalMaxPlanckResearchSchoolforComputationalBiologyandScientificComputing&FreeUniversityBerlin,DepartmentofComputerScience,Takusstrasse9,D-14195Berlin,Germanytrieglaf@inf.fu-berlin.deAbstract.Inrecentyears,ithasbe

2、comeobviousthatmRNAexpres-siondoesnotalwayscorrelatewithproteinexpression.Itseemsthatafullunderstandingofthecomplexityoflifecanonlybeobtainedbyexaminingabundancesofproteinsundervaryingconditions.Accuratemeasurementsoftheseexpressionvaluesiscrucial.Thisfieldofresearchalsorequiresnewcomputationaleffo

3、rtssincethedata,oftenfrommassspectrometryexperiments,isverycomplex.Wepresenttwoacademicsoftwareplatformsthatoffermeanstoreduce,analyseandcomparepro-teinexpressiondatagainedfromliquidchromatographycoupledwithmassspectrometry.Weoutlinetheirmethodologyandcomparethemtoourownproject,OpenMS,whichiscurre

4、ntlydevelopedinourresearchgroupattheFreeUniversityBerlinincollaborationwiththeKohlbachergroupatTuebingenUniversity.Keywords.Proteomics,quantification,softwareplatforms1IntroductionLiquidchromatographycoupledwithmassspectrometry(LC-MS)hasbeenusedextensivelytoidentifyandquantifyproteinsinasample[1].

5、Recently,thedevel-opmentofsoftwaretoolsforthequantitativeanalysisofdatafrommassspec-trometryexperimentshasarousedmuchinterest.Manydifferenttoolsarenowavailablethatimplementvariouspre-processingsuchasdenoisingandpeakpick-ingandfinallyallowtodetecttheproteinsthatwerecontainedinthesampletogetherwithan

6、estimateoftheirabundance.However,thesetoolsdifferinap-proachandscope.Somefocusonthemanagementandannotationofproteomicsdata,othersalsooffermeanstofurtherprocessandanalysethedatasets.Ingeneral,thechallengeofproteomicdataminingisthatthedataisverycom-plexandnoisy.Currently,manyprojectsrelyonratherheuri

7、stictechniquesthatdonothaveasoundtheoreticalfoundation.Ouraimistogiveabriefreviewoftwoprogramsrepresentingthecurrentstate-of-the-artinthedevelopmentofproteomicssoftwaretools.Theybothimplementaworkflowstartingfromthemass