Mass Spectrometry Data Analysis in Proteomics

445 Pages·2020·12.769 MB·English

by  Rune Matthiesen

Methods in
Molecular Biology 2051
Rune Matthiesen Editor
Mass Spectrometry
Data Analysis
in Proteomics
Third Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
Forfurther volumes:
http://www.springer.com/series/7651
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Mass Spectrometry Data
Analysis in Proteomics
Third Edition
Edited by
Rune Matthiesen
ComputationalandExperimentalBiologyGroup,CEDOC,ChronicDiseasesResearchCentre,NOVAMedical
School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
Editor
RuneMatthiesen
ComputationalandExperimental
BiologyGroup,CEDOC,Chronic
DiseasesResearchCentre,NOVA
MedicalSchool,FaculdadedeCieˆncias
Me´dicas
UniversidadeNOVAdeLisboa
Lisboa,Portugal
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9743-5 ISBN978-1-4939-9744-2 (eBook)
https://doi.org/10.1007/978-1-4939-9744-2
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Preface
The third edition of Mass Spectrometry Data Analysis in Proteomics starts as the previous
editions with a basic introduction to mass spectrometry-based proteomics. The following
chaptersarewrittenbyexpertsinspecificsubdomainsofproteomics.Theaimistoprovide
detailedinformationoneachtopictoallownewcomerstofollowthecontentbutatthesame
time present novel ideas and views that can influence future developments in mass spec-
trometry-basedproteomics.Theauthorshavebeenofferedtoprovidecompletecoverageof
theirdomainswithnopagerestriction.Thefirsteditionofthebookwaspublishedin2007,
and we have witnessed a strong improvement in sensitivity and reproducibility of mass
spectrometry-based proteomics. Furthermore, quality of computational methods has also
improved. Consequently, all chapters have been updated to provide the newest and most
relevantinformationoneachtopic.Incontrasttothepreviouseditions,thiseditionaimsto
alsoprovideinstructionsonhowtoperformthemostrelevantcomputationalmethodssuch
asdatabase-dependentsearches,althoughthefocusisstilloncomputationalconcepts.
Therearenowseveralexamplesdemonstratingthatclinicalproteomicsisreproducible,
and we and many others believe that mass spectrometry will play a major role in clinical
research in the coming years. Criticism of mass spectrometry often revolves around lack of
throughput and it will never compete with genomics because of the lack of a method to
amplify the analyte. However, clinical proteomics provides complementary information to
genomics which we refer to as proteogenomics, and several methods exist to amplify the
signal of protein-based targets. The analogy that the genome is like a cookbook for the
organismsisjustifiable.Furthermore,thesamplepreparationstepsareoftenmorestraight-
forward for mass spectrometry, and new workflows allow analysis of more than 300 blood
samples per day using a single instrument. However, to cook a delicious cake more is
needed: a good chef, functional working tools, and fresh ingredients. To answer questions
aboutthequalityofthecake,itisoftenmoreinformativetotasteitrather thanreadingthe
recipe. In fact, many diseases have a major environmental component that potentially is
better reflectedintheproteomethanthegenome.
Lisboa,Portugal RuneMatthiesen
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 IntroductiontoMassSpectrometry-BasedProteomics....................... 1
RuneMatthiesenandJakobBunkenborg
2 LC-MSSpectraProcessing............................................... 59
RuneMatthiesen
3 IsotopicDistributions ................................................... 79
AlanL.RockwoodandMagnusPalmblad
4 RetentionTimePredictionandProteinIdentification ....................... 115
AlexHennemanandMagnusPalmblad
5 ComparingPeptideSpectraMatchesAcrossSearchEngines.................. 133
RuneMatthiesen,GorkaPrieto,andHansChristianBeck
6 CalculationofFalseDiscoveryRateforPeptide
andProteinIdentification................................................ 145
GorkaPrietoandJesu´sVa´zquez
7 MethodsandAlgorithmsforQuantitativeProteomics
byMassSpectrometry ................................................... 161
RuneMatthiesenandAnaSofiaCarvalho
8 InterpretationofTandemMassSpectraofPosttranslationally
ModifiedPeptides....................................................... 199
JakobBunkenborgandRuneMatthiesen
9 SolutiontoDarkMatterIdentifiedbyMass-Tolerant
DatabaseSearch ........................................................ 231
RuneMatthiesen
10 PhosphoproteomicsProfilingtoIdentifyAlteredSignalingPathways
andKinase-TargetedCancerTherapies .................................... 241
BarnaliDeb,IreneA.George,JyotiSharma,andPrashantKumar
11 MassSpectrometry-BasedCharacterizationofUb-
andUbL-ModifiedProteins.............................................. 265
Nagore Elu,BenoitLectez,JuanmaRamirez,NereaOsinalde,
andUgoMayor
12 TargetedProteomicsasaToolforQuantifying
Urine-BasedBiomarkers................................................. 277
SonaliV.Mohan,D.S.Nayakanti,GajananSathe,
IreneA.George,HarshaGowda,andPrashantKumar
13 DataImputationinMergedIsobaricLabeling-BasedRelative
QuantificationDatasets.................................................. 297
NicolaiBjødstrupPalstrøm,RuneMatthiesen,
andHansChristianBeck
vii
viii Contents
14 ClusteringClinicalDatainR............................................. 309
AnaPina,MariaPaulaMacedo,andRobertoHenriques
15 ReviewofIssuesandSolutionstoDataAnalysisReproducibility
andDataQualityinClinicalProteomics................................... 345
MathiasWalzerandJuanAntonioVizcaı´no
16 ReviewofBatchEffectsPrevention,Diagnostics,andCorrection
Approaches ............................................................ 373
JelenaCˇuklina,PatrickG.A.Pedrioli,andRuediAebersold
17 UsingtheObject-OrientedPowerShellforSimpleProteomics
DataAnalysis........................................................... 389
YasseneMohammedandMagnusPalmblad
18 ConsiderationsintheAnalysisofHydrogenExchangeMass
SpectrometryData...................................................... 407
MichaelJ.Eggertson,KeithFadgen,JohnR.Engen,
andThomasE.Wales
Index ...................................................................... 437
Contributors
RUEDIAEBERSOLD (cid:1) DepartmentofBiology,InstituteofMolecularSystemsBiology,ETH
Zu¨rich,Zu¨rich,Switzerland;FacultyofScience,UniversityofZu¨rich,Zu¨rich,Switzerland
HANSCHRISTIANBECK (cid:1) DepartmentofClinicalBiochemistryandPharmacology,Odense
UniversityHospital,OdenseC,Denmark
JAKOB BUNKENBORG (cid:1) Alphalyse,OdenseM,Denmark
ANASOFIACARVALHO (cid:1) ComputationalandExperimentalBiologyGroup,CEDOC,Chronic
DiseasesResearchCentre,NOVAMedicalSchool,FaculdadedeCieˆnciasMe´dicas,
UniversidadeNOVAdeLisboa,Lisboa,Portugal
JELENACˇUKLINA (cid:1) DepartmentofBiology,InstituteofMolecularSystemsBiology,ETH
Zu¨rich,Zu¨rich,Switzerland;Ph.D.PrograminSystemsBiology,UniversityofZurichand
ETHZurich,Zu¨rich,Switzerland
BARNALIDEB (cid:1) InstituteofBioinformatics,InternationalTechnologyPark,Bangalore,India;
ManipalAcademyofHigherEducation(MAHE),Manipal,Karnataka,India
MICHAELJ.EGGERTSON (cid:1) WatersCorporation,Milford,MA,USA
NAGORE ELU (cid:1) DepartmentofBiochemistryandMolecularBiology,FacultyofScienceand
Technology,UniversityoftheBasqueCountry(UPV/EHU),Leioa,Spain
JOHNR.ENGEN (cid:1) DepartmentofChemistryandChemicalBiology,NortheasternUniversity,
Boston,MA,USA
KEITHFADGEN (cid:1) WatersCorporation,Milford,MA,USA
IRENE A.GEORGE (cid:1) InstituteofBioinformatics, InternationalTechnologyPark,Bangalore,
India
HARSHAGOWDA (cid:1) DepartmentofGeneticsandComputationalBiology,QIMRBerghofer
MedicalResearchInstitute,Brisbane,QLD,Australia;InstituteofBioinformatics,
Bangalore,India;ManipalAcademyofHigherEducation,Manipal,India
ALEXHENNEMAN (cid:1) Center forProteomicsandMetabolomics,LeidenUniversityMedical
Center,Leiden,TheNetherlands
ROBERTOHENRIQUES (cid:1) NOVAInformationManagementSchool(NOVAIMS),
UniversidadeNOVAdeLisboa,Lisboa,Portugal
PRASHANT KUMAR (cid:1) InstituteofBioinformatics,InternationalTechnologyPark,Bangalore,
India;ManipalAcademyofHigherEducation(MAHE),Manipal,Karnataka,India
BENOITLECTEZ (cid:1) DepartmentofBiochemistryandMolecularBiology,FacultyofScienceand
Technology,UniversityoftheBasqueCountry(UPV/EHU),Leioa,Spain
MARIAPAULAMACEDO (cid:1) CentrodeEstudosdeDoenc¸asCr(cid:1)onicas(CEDOC),NOVAMedical
School-FaculdadedeCieˆnciasMe´dicas,UniversidadeNOVAdeLisboa,Lisboa,Portugal;
DepartmentofMedicalSciences,InstituteofBiomedicine,UniversityofAveiro,Aveiro,
Portugal;APDP-DiabetesPortugalEducationandResearchCenter(APDP-ERC),
Lisboa,Portugal
RUNEMATTHIESEN (cid:1) ComputationalandExperimentalBiologyGroup,CEDOC,Chronic
DiseasesResearchCentre,NOVAMedicalSchool,FaculdadedeCieˆnciasMe´dicas,
UniversidadeNOVAdeLisboa,Lisboa,Portugal
UGOMAYOR (cid:1) DepartmentofBiochemistryandMolecularBiology,FacultyofScienceand
Technology,UniversityoftheBasqueCountry(UPV/EHU),Leioa,Spain;Ikerbasque,
BasqueFoundationforScience,Bilbao,Bizkaia,Spain
ix
x Contributors
YASSENEMOHAMMED (cid:1) Center forProteomicsandMetabolomics,LeidenUniversityMedical
Center,Leiden,TheNetherlands;UniversityofVictoria–GenomeBritishColumbia
ProteomicsCentre,Victoria,BC,Canada
SONALIV.MOHAN (cid:1) DepartmentofGeneticsandComputationalBiology,QIMRBerghofer
MedicalResearchInstitute,Brisbane,QLD,Australia;InstituteofBioinformatics,
Bangalore,India;ManipalAcademyofHigherEducation,Manipal,India
D.S.NAYAKANTI (cid:1) InstituteofBioinformatics, Bangalore,India;ManipalAcademyof
HigherEducation,Manipal,India
NEREAOSINALDE (cid:1) DepartmentofBiochemistryandMolecularBiology,FacultyofPharmacy,
UniversityoftheBasqueCountry(UPV/EHU),Vitoria-Gasteiz,Spain
MAGNUSPALMBLAD (cid:1) Center forProteomicsandMetabolomics,LeidenUniversityMedical
Center,Leiden,TheNetherlands
NICOLAI BJØDSTRUPPALSTRØM (cid:1) DepartmentofClinicalBiochemistryandPharmacology,
OdenseUniversityHospital,OdenseC,Denmark
PATRICKG.A.PEDRIOLI (cid:1) DepartmentofBiology,InstituteofMolecularSystemsBiology,
ETHZu¨rich,Zu¨rich,Switzerland;ETHZu¨rich,PHRT-MS,Zu¨rich,Switzerland
ANAPINA (cid:1) CentrodeEstudosdeDoenc¸asCr(cid:1)onicas(CEDOC),NOVAMedicalSchool-
FaculdadedeCieˆnciasMe´dicas,UniversidadeNOVAdeLisboa,Lisboa,Portugal;
ProRegeMPhDProgramme,NOVAMedicalSchool/FaculdadedeCieˆnciasMe´dicas,
UniversidadeNOVAdeLisboa,Lisboa,Portugal;DepartmentofMedicalSciences,
InstituteofBiomedicine,UniversityofAveiro,Aveiro,Portugal
GORKAPRIETO (cid:1) DepartmentofCommunicationsEngineering,FacultyofEngineeringof
Bilbao,UniversityoftheBasqueCountry(UPV/EHU),Bilbao,Spain
JUANMARAMIREZ (cid:1) DepartmentofBiochemistryandMolecularBiology,FacultyofScience
andTechnology,UniversityoftheBasqueCountry(UPV/EHU),Leioa,Spain
ALANL.ROCKWOOD (cid:1) DepartmentofPathology,UniversityofUtah,SaltLakeCity,UT,
USA
GAJANANSATHE (cid:1) InstituteofBioinformatics,Bangalore,India;ManipalAcademyofHigher
Education,Manipal,India
JYOTISHARMA (cid:1) InstituteofBioinformatics,InternationalTechnologyPark,Bangalore,
India;ManipalAcademyofHigherEducation(MAHE),Manipal,Karnataka,India
JESU´SVA´ZQUEZ (cid:1) LaboratoryofCardiovascularProteomics,CentroNacionalde
InvestigacionesCardiovasculares(CNIC)andCIBERdeEnfermedadesCardiovasculares
(CIBERCV),Madrid,Spain
JUANANTONIO VIZCAI´NO (cid:1) EuropeanMolecularBiologyLaboratory,European
BioinformaticsInstitute(EMBL-EBI),Cambridge,UK
THOMASE.WALES (cid:1) DepartmentofChemistryandChemicalBiology,Northeastern
University,Boston,MA,USA
MATHIASWALZER (cid:1) EuropeanMolecularBiologyLaboratory,EuropeanBioinformatics
Institute(EMBL-EBI),Cambridge,UK