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Methods in Molecular Biology 2603 Jose L. Luque-Garcia Editor Methods and Protocols 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 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. SILAC Methods and Protocols Edited by Jose L. Luque-Garcia Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain Editor JoseL.Luque-Garcia AnalyticalChemistryDepartment FacultyofChemicalSciences ComplutenseUniversityofMadrid Madrid,Spain ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-2862-1 ISBN978-1-0716-2863-8 (eBook) https://doi.org/10.1007/978-1-0716-2863-8 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerScience+BusinessMedia,LLC,part ofSpringerNature2023 Thisworkissubjecttocopyright.AllrightsaresolelyandexclusivelylicensedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,reproductionon microfilmsorinanyotherphysicalway,andtransmissionorinformation storageand retrieval,electronicadaptation, computersoftware,orbysimilar ordissimilar methodologynow knownorhereafter developed. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface SILAC,orstableisotopelabelingbyaminoacidsincellculture,wasproposedabout20years ago as a new tool for the quantification of differentially expressed proteins. Since then, SILAChasestablisheditselfasafundamentaltechniqueintheareaoffunctionalproteomics, given its enormous versatility and high accuracy compared to other strategies for protein quantification.Thepotentialofthisanalyticalstrategyhasincreasedovertheyearsthanksto thedevelopmentofnewtechnologiesinthefieldofmassspectrometryandbioinformatics, but undoubtedly also thanks to the ingenuity of numerous researchers who, through modifications of the original protocol, have greatly expanded its field of application. Such isthecasethat,tothisday,SILACcanbeconsideredthefirsttoolofchoiceinquantitative proteomics either on its own or in combination with other more recently developed approaches. The chief purpose of this book, which can be considered a continuation of anotherbookonthesametopicpublishedin2014inthissameseriesandeditedbyBettina Warscheid, has been to collect the main SILAC-based methods developed since then, in ordertoprovidereaderswithdetailedprotocolsfortheirsuccessfulapplication.Iwouldfirst like to thank the senior editor of the series for his initial suggestion and, especially, all the authors who have contributed to this book for their generosity and invaluable help in the processofputtingittogether. Madrid,Spain JoseL.Luque-Garcia v Contents Preface ..................................................................... v Contributors................................................................. ix 1 DynamicSILACtoDetermineProteinTurnoverinNeuronsandGlia ........ 1 AlineR.Dörrbaum,ErinM.Schuman,andJulianD.Langer 2 SILAC-BasedProteomicAnalysisofMeiosisintheFissionYeast Schizosaccharomycespombe... ........ ....... ....... ........ ....... ........ 19 DorotheaAnrather,SilviaBagelovaPolakova, LubosCipak,andJurajGregan 3 IdentificationofProteinInteractionPartnersinBacteriaUsingAffinity PurificationandSILACQuantitativeProteomics .... ........ ....... ........ 31 MonikaKopeckova,MarekLink,andIvonaPavkova 4 pSILAC-BasedDeterminationofCellularProteinSorting intoExtracellularVesicles ........... ....... ....... .... .... ...... ....... .. 43 So-FongCamNgan,NeilE.McCarthy,andSiuKwanSze 5 QuantificationofProteinPalmitoylationbyCysteine-SILAC......... ........ 59 CaiyunFang,XiaoqinZhang,andHaojieLu 6 ComparativeSUMOProteomeAnalysisUsingStableIsotopicLabeling byAminoAcids(SILAC) ........... ....... ....... ........ ....... ........ 71 GeorgiaChachamiandSina-VictoriaBarysch 7 ASuper-SILACApproachforProfilingHistonePosttranslational Modifications....... ....... ........ ....... .... ... ...... .. ... .... ........ 87 RobertaNoberini,ElisaLonghi,andTizianaBonaldi 8 SILAC-BasedQuantitativePhosphoproteomicsinYeast ...... ....... ........ 103 MarıáLuisaHernaézandConchaGil 9 PhosphotyrosineProfilingUsingSILAC..... ....... ........ ....... ........ 117 KeshavaK.Datta,AditiChatterjee,andHarshaGowda 10 ChemoproteomicProfilingofGeranylPyrophosphate-BindingProteins....... 127 RongCaiandYinshengWang 11 QuantitativeAnalysisoftheEndoplasmicReticulum-AssociatedProteins UsingER-LocalizableReactiveMolecules .......... ........ ...... ..... .... 139 TomonoriTamuraandItaruHamachi 12 WorkflowforQuantitativeProteomicAnalysisofIntestinalOrganoids UsingSILAC....... ....... ........ ....... ....... ........ ....... ........ 151 AlexisGonneaud,ClaudeAsselin,Ve´roniqueGiroux, andFrançois-MichelBoisvert vii viii Contents 13 StableIsotopeLabelingbyAminoAcidsandBioorthogonalNoncanonical AminoAcidTagginginCulturedPrimaryNeurons.......... ....... ........ 163 GuoanZhang,KatrinDeinhardt,andThomasA.Neubert 14 HeavyMethylSILACMetabolicLabelingofHumanCellLines forHigh-ConfidenceIdentificationofR/K-MethylatedPeptides byHigh-ResolutionMassSpectrometry ..... ....... ........ ....... ........ 173 EnricoMassignani,MariannaManiaci,andTizianaBonaldi 15 SILAC-BasedQuantitativeProteomicAnalysisofDrosophilaEmbryos........ 187 AlistairLanglands,HamzeBeati,andH.-ArnoJ.Mu¨ller 16 Super-SILACQuantitativeProteomeProfilingofZebrafishLarvae ........... 199 GuillermoAragoneses-Cazorla,AndresMachuca, M.PilarBuendia-Nacarino,DanielaS.Anunciaçaõ, EstefaniaGarcia-Calvo,andJoseL.Luque-Garcia 17 UseofNuclearandChromatinEnrichmentProceduresforQuantitation ofYeastDNAReplicationProteinsUsingSILAC.... ........ ....... ........ 209 TakashiKubota 18 CombinationofStableIsotopeLabelingbyAminoAcidsinCellCulture (SILAC)andSubstrateTrappingfor theDetectionofTransient ProteinInteractions........ ........ ....... ....... ........ ....... ........ 219 JoleneM.DudaandStefaniN.Thomas 19 ProfilingofSecretedProteinsinSerum-ContainingMedia UsingBONCATandPulsedSILAC......... ....... ........ ....... ........ 235 JihyeShinandCheoljuLee 20 UsingSILACtoDevelopQuantitativeData-IndependentAcquisition (DIA)ProteomicMethods.......... ....... ....... ...... ......... ........ 245 EllenP.Casavant,JasonLiang,SumedhSankhe, W.RodneyMathews,andVeronicaG.Anania 21 SILAC-IodoTMTforAssessmentoftheCellularProteome andItsRedoxStatus ....... ........ ....... ....... ........ ....... ........ 259 MarieVajrychova,BarboraSalovska,KristynaPimkova, IvoFabrik,andZdenekHodny 22 TargetedAbsoluteProteinQuantificationUsingSILACInternalStandard andFull-LengthProteinCalibrators(TAQSI)....... ........ ....... ........ 269 XinwenWang,JianShi,andHao-JieZhu Index ...................................................................... 285 Contributors VERONICAG.ANANIA • Genentech,SouthSanFrancisco,CA,USA DOROTHEAANRATHER • MassSpectrometryFacility,MaxPerutzLabs,ViennaBioCenter (VBC),Vienna,Austria DANIELA S.ANUNCIAÇAÕ • InstitutodeQuı´micaeBiotecnologia,UniversidadeFederalde Alagoas,Macei(cid:1)o,AL,Brazil GUILLERMOARAGONESES-CAZORLA • AnalyticalChemistryDepartment,FacultyofChemical Sciences,ComplutenseUniversityofMadrid,Madrid,Spain CLAUDEASSELIN • DepartmentofImmunologyandCellBiology,AppliedCancerResearch Pavilion,FacultyofMedicineandHealthSciences,Universite´deSherbrooke,QC,Canada SINA-VICTORIABARYSCH • Zentrumfu¨rMolekulareBiologiederUniversita€tHeidelberg (ZMBH),DKFZ-ZMBHAlliance,HeidelbergUniversity,Heidelberg,Germany;EMBL Heidelberg,Heidelberg,Germany HAMZE BEATI • DevelopmentalGeneticsGroup,InstituteforBiology,UniversityofKassel, Kassel,Germany FRANÇOIS-MICHELBOISVERT • DepartmentofImmunologyandCellBiology,AppliedCancer ResearchPavilion,FacultyofMedicineandHealthSciences,Universite´deSherbrooke,QC, Canada TIZIANABONALDI • DepartmentofExperimentalOncology,IEO,EuropeanInstituteof OncologyIRCCS,Milan,Italy;DepartmentofExperimentalOncology,IEO,European InstituteofOncologyIRCCS,Milan,Italy; DepartmentofOncologyandHaemathology- Oncology,UniversityofMIlan,Milano,Italy M.PILARBUENDIA-NACARINO • AnalyticalChemistryDepartment,FacultyofChemical Sciences,ComplutenseUniversityofMadrid,Madrid,Spain RONGCAI • InstituteofPharmaceuticalAnalysis,KeyLaboratoryofChemicalBiology (MOE),SchoolofPharmaceuticalSciences,CheelooCollegeofMedicine,Shandong University,Jinan,Shandong,China ELLENP.CASAVANT • Genentech,SouthSanFrancisco,CA,USA GEORGIACHACHAMI • LaboratoryofBiochemistry,FacultyofMedicine,Universityof Thessaly,Larissa,Greece ADITICHATTERJEE • InstituteofBioinformatics,Bangalore,India LUBOSCIPAK • CancerResearchInstitute,BiomedicalResearchCenter,SlovakAcademyof Sciences,Bratislava,Slovakia KESHAVAK.DATTA • DepartmentofGeneticsandComputationalBiology,QIMRBerghofer MedicalResearchInstitute,Brisbane,QLD,Australia KATRINDEINHARDT • InstituteforLifeSciencesandCentreforBiologicalSciences,University ofSouthampton,Southampton,UK ALINE R.DO¨RRBAUM • MaxPlanckInstituteforBrainResearch,FrankfurtamMain, Germany JOLENEM.DUDA • DepartmentofBiochemistry,MolecularBiologyandBiophysics, UniversityofMinnesotaCollegeofBiologicalSciences,Minneapolis,MN,USA IVOFABRIK • BiomedicalResearchCenter,UniversityHospitalHradecKralove,Hradec Kralove,CzechRepublic CAIYUNFANG • DepartmentofChemistry,FudanUniversity,Shanghai,China ix x Contributors ESTEFANIAGARCIA-CALVO • AnalyticalChemistryDepartment,FacultyofChemicalSciences, ComplutenseUniversityofMadrid,Madrid,Spain CONCHAGIL • UnidaddeProte(cid:1)omica,FacultaddeFarmacia,UniversidadComplutensede Madrid,Madrid,Spain;DepartamentodeMicrobiologıáyParasitologıá.Facultadde Farmacia,UniversidadComplutensedeMadrid,Madrid,Spain VE´RONIQUEGIROUX • DepartmentofImmunologyandCellBiology,AppliedCancer ResearchPavilion,FacultyofMedicineandHealthSciences,Universite´deSherbrooke,QC, Canada ALEXISGONNEAUD • DepartmentofImmunologyandCellBiology,AppliedCancerResearch Pavilion,FacultyofMedicineandHealthSciences,Universite´deSherbrooke,QC,Canada HARSHAGOWDA • DepartmentofGeneticsandComputationalBiology,QIMRBerghofer MedicalResearchInstitute,Brisbane,QLD,Australia;SchoolofBiomedicalSciences,The UniversityofQueensland,Brisbane,QLD,Australia;FacultyofHealth,Queensland UniversityofTechnology,Brisbane,QLD,Australia JURAJGREGAN • AdvancedMicroscopyFacility,VBCFandDepartmentofChromosome Biology,MaxPerutzLabs,UniversityofVienna,ViennaBioCenter(VBC),Vienna, Austria ITARUHAMACHI • DepartmentofSyntheticChemistryandBiologicalChemistry,Graduate SchoolofEngineering,KyotoUniversity,Nishikyo-ku,Kyoto,Japan;ERATO(Exploratory ResearchforAdvancedTechnology,JST),Chiyodaku,Tokyo,Japan MARIÁLUISAHERNAÉZ • UnidaddeProte(cid:1)omica,FacultaddeFarmacia,Universidad ComplutensedeMadrid,Madrid,Spain ZDENEK HODNY • DepartmentofGenomeIntegrity,InstituteofMolecularGeneticsofthe CzechAcademyofScience,Prague,CzechRepublic MONIKAKOPECKOVA • UniversityofDefence,FacultyofMilitaryHealthSciences, DepartmentofMolecularPathologyandBiology,HradecKralove,CzechRepublic TAKASHIKUBOTA • InstituteofMedicalSciences,SchoolofMedicine,MedicalSciences& Nutrition,UniversityofAberdeen,Aberdeen,Scotland,UK JULIAN D.LANGER • MaxPlanckInstituteforBrainResearch,FrankfurtamMain, Germany;MaxPlanckInstituteofBiophysics,FrankfurtamMain,Germany ALISTAIRLANGLANDS • NationalPhenotypicScreeningCentre,SchoolofLifeSciences, UniversityofDundee,Dundee,UK CHEOLJULEE • Center forTheragnosis,KoreaInstituteofScienceandTechnology,Seoul, Korea;DivisionofBio-MedicalScience&Technology,KISTSchool,KoreaUniversityof ScienceandTechnology,Seoul,Korea JASON LIANG • Genentech,SouthSanFrancisco,CA,USA MAREKLINK • UniversityofDefence,FacultyofMilitaryHealthSciences,Departmentof MolecularPathologyandBiology,HradecKralove,CzechRepublic ELISALONGHI • DepartmentofExperimentalOncology,IEO,EuropeanInstituteofOncology IRCCS,Milan,Italy HAOJIELU • DepartmentofChemistryandInstitutesofBiomedicalSciences,Fudan University,Shanghai,China JOSEL.LUQUE-GARCIA • AnalyticalChemistryDepartment,FacultyofChemicalSciences, ComplutenseUniversityofMadrid,Madrid,Spain