Mass Spectrometry Data Analysis in Proteomics

407 Pages·2013·7.899 MB·English

by  Rune Matthiesen, Jakob Bunkenborg (auth.), Rune Matthiesen (eds.)

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
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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
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