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Mass Spectrometry Data Analysis in Proteomics PDF

407 Pages·2013·7.899 MB·English
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Methods in Molecular Biology 1007 Rune Matthiesen Editor Mass Spectrometry Data Analysis in Proteomics Second Edition M M B TM ETHODS IN OLECULAR IOLOGY SeriesEditor JohnM.Walker School ofLife Sciences University ofHertfordshire Hatfield, Hertfordshire,AL109AB,UK For further volumes: http://www.springer.com/series/7651 . Mass Spectrometry Data Analysis in Proteomics Second Edition Edited by Rune Matthiesen Institute of Molecular Pathology and Immunology Universidade do Porto, Porto, Portugal Editor RuneMatthiesen InstituteofMolecularpathology andImmunology UniversidadedoPorto Porto,Portugal ISSN1064-3745 ISSN1940-6029(electronic) ISBN978-1-62703-391-6 ISBN978-1-62703-392-3(eBook) DOI10.1007/978-1-62703-392-3 SpringerNewYorkHeidelbergDordrechtLondon LibraryofCongressControlNumber:2013934714 ªSpringerScience+BusinessMedia,LLC2013 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.Exemptedfromthis legalreservationarebriefexcerptsinconnectionwithreviewsorscholarlyanalysisormaterialsuppliedspecificallyfor thepurposeofbeingenteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework. DuplicationofthispublicationorpartsthereofispermittedonlyundertheprovisionsoftheCopyrightLawofthe Publisher’slocation,initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Permissions forusemaybeobtainedthroughRightsLinkattheCopyrightClearanceCenter.Violationsareliabletoprosecution undertherespectiveCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnot imply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsand regulationsandthereforefreeforgeneraluse. Whiletheadviceandinformationinthisbookarebelievedtobetrueandaccurateatthedateofpublication,neitherthe authorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityforanyerrorsoromissionsthatmaybe made.Thepublishermakesnowarranty,expressorimplied,withrespecttothematerialcontainedherein. Printedonacid-freepaper HumanaPressisabrandofSpringer SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Thisbookhasbeenpreparedtostartoutwithabasicintroductiontomassspectrometry-based proteomics.Theintroductorychapterisfollowedbychapterswrittenbyexpertsinspecific subdomainsofMS-basedproteomics.TheexpertspresenttheirviewonspecificMS-based methodsordataanalysisstrategiesinproteomics.Thebookiswrittenwiththepurposeof coveringspecifictopicsindetailrather thanglossingover thetopic.Detaileddiscussionis madepossiblesinceSpringerallowednopagerestrictionontheexperts’chapters. This is the second edition of the book, and, in the 6 years since the publishing of the first edition, the instrumentation and methods have been considerably improved. My personal experience as editor has also been enhanced. I promise the reader that much effort and time have been devoted to making the book up-to-date, and, in fact, every single chapter is either new or has been completely rewritten. I have no doubt that this book is useful for everyone working in proteomics. I have to thank the many invited authors for their on-time delivery and detailed chapters. The authors have provided originalmanuscriptsandevennovelconceptsinsomecases.Thebookcoversdataanalysis topics relevant for quantitative proteomics, posttranslational modification, HX-MS, glycomics,anddataexchangestandards. Porto,Portugal RuneMatthiesen v Contents Preface ................................................................... v Contributors............................................................... ix 1 IntroductiontoMassSpectrometry-BasedProteomics..................... 1 RuneMatthiesenandJakobBunkenborg 2 LC-MSSpectraProcessing ............................................. 47 RuneMatthiesen 3 IsotopicDistributions.................................................. 65 AlanL.RockwoodandMagnusPalmblad 4 RetentionTimePredictionandProteinIdentification...................... 101 AlexA.HennemanandMagnusPalmblad 5 AlgorithmsforDatabase-DependentSearchofMS/MSData............... 119 RuneMatthiesen 6 InterpretationofTandemMassSpectraofPosttranslationally ModifiedPeptides..................................................... 139 JakobBunkenborgandRuneMatthiesen 7 ImprovingPeptideIdentificationUsingEmpiricalScoringSystems.......... 173 RobertJ.Chalkley 8 MethodsandAlgorithmsforQuantitativeProteomics byMassSpectrometry.................................................. 183 RuneMatthiesenandAnaSofiaCarvalho 9 ComputationalApproachestoSelectedReaction MonitoringAssayDesign............................................... 219 ConradBessantandJunFan 10 FeatureSelectionandMachineLearningwithMassSpectrometryData...... 237 SusmitaDatta 11 ConsiderationsintheAnalysisofHydrogenExchange MassSpectrometryData ............................................... 263 ThomasE.Wales,MichaelJ.Eggertson,andJohnR.Engen 12 PermethylatedN-GlycanAnalysiswithMassSpectrometry ................. 289 ZhenxinLinandDavidM.Lubman 13 MassSpectrometryMethodsforStudyingGlycosylationinCancer.......... 301 HugoOso´rioandCelsoA.Reis 14 ProteomicsDataExchangeandStorage:TheNeedforCommon StandardsandPublicRepositories....................................... 317 RafaelC.Jime´nezandJuanAntonioVizcaı´no 15 ToolsforProteinPosttranslationalModificationsAnalysis: FAK,aCaseStudy..................................................... 335 CatarinaFonseca,PaulaVoabil,AnaSofiaCarvalho, andRuneMatthiesen vii viii Contents 16 ProteomicStrategiestoCharacterizeSignalingPathways................... 359 H.C.Harsha,SnehaM.Pinto,andAkhileshPandey 17 SimpleProteomicsDataAnalysisintheObject-OrientedPowerShell........ 379 YasseneMohammedandMagnusPalmblad Appendices................................................................ 393 Index..................................................................... 401 Contributors CONRADBESSANT (cid:1) SchoolofBiologicalandChemicalSciences,QueenMary UniversityofLondon,London,UK JAKOB BUNKENBORG (cid:1) DepartmentofBiochemistryandMolecularBiology, UniversityofSouthernDenmark,OdenseM,Denmark ANASOFIACARVALHO (cid:1) InstituteofMolecularPathologyandImmunology oftheUniversityofPorto(IPATIMUP),Porto,Portugal ROBERTJ.CHALKLEY (cid:1) DepartmentofPharmaceuticalChemistry, UniversityofCaliforniaSanFrancisco,SanFrancisco,CA,USA SUSMITADATTA (cid:1) DepartmentofBioinformatics andBiostatistics,SchoolofPublic HealthandInformationSciences,UniversityofLouisville,Louisville,KY,USA MICHAELJ.EGGERTSON (cid:1) WatersCorporation,Milford,MA,USA JOHNR.ENGEN (cid:1) DepartmentofChemistryandChemicalBiology,Northeastern University,Boston,MA,USA JUNFAN (cid:1) SchoolofBiologicalandChemicalSciences,QueenMaryUniversityof London,London,UK CATARINAFONSECA (cid:1) InstituteofMolecularPathologyandImmunology oftheUniversityofPorto(IPATIMUP),Porto,Portugal H.C.HARSHA (cid:1) InstituteofBioinformatics,InternationalTechnologyPark, Bangalore,India ALEXA.HENNEMAN (cid:1) Center forProteomicsandMetabolomics,LeidenUniversity MedicalCenter,Leiden,TheNetherlands RAFAELC.JIME´NEZ (cid:1) EMBL-EBI,Hinxton,Cambridge,UK ZHENXINLIN (cid:1) DepartmentofChemistry,UniversityofMichigan, AnnArbor,MI,USA DAVIDM.LUBMAN (cid:1) DepartmentofSurgery,UniversityofMichigan, AnnArbor,MI,USA RUNEMATTHIESEN (cid:1) InstituteofMolecularPathologyandImmunology oftheUniversityofPorto(IPATIMUP),Porto,Portugal YASSENEMOHAMMED (cid:1) Center forProteomicsandMetabolomics,LeidenUniversity MedicalCenter,Leiden,TheNetherlands HUGOOSO´RIO (cid:1) InstituteofMolecularPathologyandImmunologyoftheUniversity ofPorto(IPATIMUP),Porto,Portugal;FacultyofMedicine,UniversityofPorto, Porto,Portugal MAGNUSPALMBLAD (cid:1) Center forProteomicsandMetabolomics,LeidenUniversity MedicalCenter,Leiden,TheNetherlands AKHILESH PANDEY (cid:1) DepartmentsofBiologicalChemistry,Pathology,andOncology, McKusick-NathansInstituteofGeneticMedicine,JohnsHopkinsUniversity, Baltimore,MD,USA SNEHAM.PINTO (cid:1) InstituteofBioinformatics, InternationalTechnologyPark, Bangalore,India CELSOA.REIS (cid:1) InstituteofMolecularPathologyandImmunologyoftheUniversity ofPorto(IPATIMUP),Porto,Portugal;FacultyofMedicine,InstituteofBiomedical SciencesofAbelSalazar(ICBAS),UniversityofPorto,Porto,Portugal ix

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