Quantitative Proteomics
As a component of post-genome science, the field of proteomics has assumed great prominence in recent years. Whereas quantitative analyses focussed initially on relative quantification, a greater emphasis is now placed on absolute quantification and consideration of proteome dynamics. Coverage of the topic of quantitative proteomics requires consideration both of the analytical fundamentals of quantitative mass spectrometry and the specific demands of the problem being addressed.
Quantitative Proteomics aims to outline the state of the art in mass spectrometry-based quantitative proteomics, describing recent advances and current limitations in the instrumentation used, together with the various methods employed for generating high quality data. Details on both strategies describing how stable isotope labelling can be applied and methods for performing quantitative analysis of proteins in a label-free manner are given. The utility of these strategies to understanding cellular protein dynamics are then exemplified with chapters looking at spatial proteomics, dynamics of protein function as determined by quantifying changes in protein post-translational modification and protein turnover. Finally, a key application of these techniques to biomarker discovery and validation is presented, together with the rapidly developing area of quantitative analysis of protein-based foodstuffs.
This exemplary book is essential reading for analytical and biological mass spectrometrists working in proteomics research, as well as those undertaking either fundamental or clinical-based investigations with an interest in understanding protein dynamics and/or biomarker assessment.
Quantitative Proteomics, The Royal Society of Chemistry, 2014.
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CHAPTER 1: Practical Considerations and Current Limitations in Quantitative Mass Spectrometry-based Proteomicsp1-25ByAdam M. HawkridgeAdam M. HawkridgeDepartments of Pharmaceutics & Pharmacotherapy and Outcomes Sciences, Virginia Commonwealth University School of PharmacyRichmondVA 23298USAamhawkridge@vcu.eduSearch for other works by this author on:
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CHAPTER 2: High Resolution/Accurate Mass Targeted Proteomicsp26-47ByB. DomonB. DomonSearch for other works by this author on:
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CHAPTER 3: Making Sense Out of the Proteome: the Utility of iTRAQ and TMTp49-79ByNarciso Couto;Narciso CoutoChELSI Institute, Department of Chemical and Biological Engineering, University of SheffieldMappin StreetSheffieldS1 3JDUKcaroline.evans@sheffield.ac.ukSearch for other works by this author on:Caroline A. Evans;Caroline A. EvansChELSI Institute, Department of Chemical and Biological Engineering, University of SheffieldMappin StreetSheffieldS1 3JDUKcaroline.evans@sheffield.ac.ukSearch for other works by this author on:Jagroop Pandhal;Jagroop PandhalChELSI Institute, Department of Chemical and Biological Engineering, University of SheffieldMappin StreetSheffieldS1 3JDUKcaroline.evans@sheffield.ac.ukSearch for other works by this author on:Wen Qiu;Wen QiuChELSI Institute, Department of Chemical and Biological Engineering, University of SheffieldMappin StreetSheffieldS1 3JDUKcaroline.evans@sheffield.ac.ukSearch for other works by this author on:Trong K. Pham;Trong K. PhamChELSI Institute, Department of Chemical and Biological Engineering, University of SheffieldMappin StreetSheffieldS1 3JDUKcaroline.evans@sheffield.ac.ukSearch for other works by this author on:Josselin Noirel;Josselin NoirelChELSI Institute, Department of Chemical and Biological Engineering, University of SheffieldMappin StreetSheffieldS1 3JDUKcaroline.evans@sheffield.ac.ukSearch for other works by this author on:Phillip C. WrightPhillip C. WrightChELSI Institute, Department of Chemical and Biological Engineering, University of SheffieldMappin StreetSheffieldS1 3JDUKcaroline.evans@sheffield.ac.ukSearch for other works by this author on:
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CHAPTER 4: Getting Absolute: Determining Absolute Protein Quantities via Selected Reaction Monitoring Mass Spectrometryp80-109ByChristina Ludwig;Christina LudwigInstitute of Molecular Systems Biology, Department of Biology, ETH Zurich8093 ZurichSwitzerlandSearch for other works by this author on:Ruedi AebersoldRuedi AebersoldInstitute of Molecular Systems Biology, Department of Biology, ETH Zurich8093 ZurichSwitzerlandSearch for other works by this author on:
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CHAPTER 5: Proteomics Standards with Controllable Trueness—Absolute Quantification of Peptides, Phosphopeptides and Proteins Using ICP- and ESI-MSp110-128ByAnna Konopka;Anna KonopkaMolecular Structure Analysis, German Cancer Research Center (DKFZ)HeidelbergGermanywolf.lehmann@dkfz.deSearch for other works by this author on:Christina Wild;Christina WildMolecular Structure Analysis, German Cancer Research Center (DKFZ)HeidelbergGermanywolf.lehmann@dkfz.deSearch for other works by this author on:Martin E. Boehm;Martin E. BoehmMolecular Structure Analysis, German Cancer Research Center (DKFZ)HeidelbergGermanywolf.lehmann@dkfz.deSearch for other works by this author on:Wolf D. LehmannWolf D. LehmannMolecular Structure Analysis, German Cancer Research Center (DKFZ)HeidelbergGermanywolf.lehmann@dkfz.deSearch for other works by this author on:
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CHAPTER 6: Overview and Implementation of Mass Spectrometry-Based Label-Free Quantitative Proteomicsp129-153ByErik J. Soderblom;Erik J. SoderblomProteomics Core Facility, Institute for Genome Science & Policy, Duke University Medical CenterDurhamNCUSAerik.soderblom@duke.eduSearch for other works by this author on:J. Will Thompson;J. Will ThompsonProteomics Core Facility, Institute for Genome Science & Policy, Duke University Medical CenterDurhamNCUSAerik.soderblom@duke.eduSearch for other works by this author on:M. Arthur MoseleyM. Arthur MoseleyProteomics Core Facility, Institute for Genome Science & Policy, Duke University Medical CenterDurhamNCUSAerik.soderblom@duke.eduSearch for other works by this author on:
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CHAPTER 7: MS1 Label-free Quantification Using Ion Intensity Chromatograms in Skyline (Research and Clinical Applications)p154-174ByBirgit Schilling;Birgit SchillingBuck Institute for Research on Aging8001 Redwood BoulevardNovatoCalifornia 94945USAbschilling@buckinstitute.orgSearch for other works by this author on:Brendan X. MacLean;Brendan X. MacLeanUniversity of Washington, Department of Genome SciencesFoege Building S1133720 15th Ave NESeattleWA 98195USAbgibson@buckinstitute.orgSearch for other works by this author on:Alexandria D'Souza;Alexandria D'SouzaBuck Institute for Research on Aging8001 Redwood BoulevardNovatoCalifornia 94945USAbschilling@buckinstitute.orgSearch for other works by this author on:Matthew J. Rardin;Matthew J. RardinBuck Institute for Research on Aging8001 Redwood BoulevardNovatoCalifornia 94945USAbschilling@buckinstitute.orgSearch for other works by this author on:Nicholas J. Shulman;Nicholas J. ShulmanUniversity of Washington, Department of Genome SciencesFoege Building S1133720 15th Ave NESeattleWA 98195USAbgibson@buckinstitute.orgSearch for other works by this author on:Michael J. MacCoss;Michael J. MacCossUniversity of Washington, Department of Genome SciencesFoege Building S1133720 15th Ave NESeattleWA 98195USAbgibson@buckinstitute.orgSearch for other works by this author on:Bradford W. GibsonBradford W. GibsonBuck Institute for Research on Aging8001 Redwood BoulevardNovatoCalifornia 94945USAbschilling@buckinstitute.orgSearch for other works by this author on:
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CHAPTER 8: Label-free Quantification of Proteins Using Data-Independent Acquisitionp175-184ByYishai LevinYishai LevinProteomics Unit, Israel National Center for Personalized Medicine, Weizmann Institute of ScienceRehovot 76100Israelyishai.levin@weizmann.ac.ilSearch for other works by this author on:
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CHAPTER 9: Spatial Proteomics: Practical Considerations for Data Acquisition and Analysis in Protein Subcellular Localisation Studiesp185-210ByAndy Christoforou;Andy ChristoforouCambridge Centre for Proteomics, Department of Biochemistry, University of CambridgeUnited KingdomCB2 1QRk.s.lilley@bioc.cam.ac.ukSearch for other works by this author on:Claire Mulvey;Claire MulveyCambridge Centre for Proteomics, Department of Biochemistry, University of CambridgeUnited KingdomCB2 1QRk.s.lilley@bioc.cam.ac.ukSearch for other works by this author on:Lisa M. Breckels;Lisa M. BreckelsCambridge Centre for Proteomics, Department of Biochemistry, University of CambridgeUnited KingdomCB2 1QRk.s.lilley@bioc.cam.ac.ukSearch for other works by this author on:Laurent Gatto;Laurent GattoCambridge Centre for Proteomics, Department of Biochemistry, University of CambridgeUnited KingdomCB2 1QRk.s.lilley@bioc.cam.ac.ukSearch for other works by this author on:Kathryn S. LilleyKathryn S. LilleyCambridge Centre for Proteomics, Department of Biochemistry, University of CambridgeUnited KingdomCB2 1QRk.s.lilley@bioc.cam.ac.ukSearch for other works by this author on:
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CHAPTER 10: Quantitative Analyses of Phosphotyrosine Cellular Signaling in Diseasep211-232ByHannah JohnsonHannah JohnsonDepartment of Biological Engineering, Massachusetts Institute of TechnologyCambridgeMA 02139USAhjohnsn@mit.eduSearch for other works by this author on:
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CHAPTER 11: Next Generation Proteomics: PTMs in Space and Timep233-256ByDalila Bensadek;Dalila BensadekCentre for Gene Regulation & Expression, College of Life Sciences, University of DundeeDow StreetDundeeDD1 5EHUnited Kingdoma.i.lamond@dundee.ac.ukSearch for other works by this author on:Armel Nicolas;Armel NicolasCentre for Gene Regulation & Expression, College of Life Sciences, University of DundeeDow StreetDundeeDD1 5EHUnited Kingdoma.i.lamond@dundee.ac.ukSearch for other works by this author on:Angus I. LamondAngus I. LamondCentre for Gene Regulation & Expression, College of Life Sciences, University of DundeeDow StreetDundeeDD1 5EHUnited Kingdoma.i.lamond@dundee.ac.ukSearch for other works by this author on:
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CHAPTER 12: Experimental and Analytical Approaches to the Quantification of Protein Turnover on a Proteome-wide Scalep257-276ByAmy J. Claydon;Amy J. ClaydonProtein Function Group, Institute of Integrative Biology, University of LiverpoolLiverpoolL69 7ZBUKR.Beynon@liverpool.ac.ukSearch for other works by this author on:Dean E. Hammond;Dean E. HammondProtein Function Group, Institute of Integrative Biology, University of LiverpoolLiverpoolL69 7ZBUKR.Beynon@liverpool.ac.ukSearch for other works by this author on:Robert J. BeynonRobert J. BeynonProtein Function Group, Institute of Integrative Biology, University of LiverpoolLiverpoolL69 7ZBUKR.Beynon@liverpool.ac.ukSearch for other works by this author on:
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CHAPTER 13: Protein Quantification by MRM for Biomarker Validationp277-315ByL. Staunton;L. StauntonUCD Conway Institute, School of Medicine and Medical Science, University College DublinDublin 4IrelandSearch for other works by this author on:T. Clancy;T. ClancyDepartment of Tumor Biology, Institute for Cancer Research, Oslo University HospitalNorwaySearch for other works by this author on:C. Tonry;C. TonryUCD Conway Institute, School of Medicine and Medical Science, University College DublinDublin 4IrelandSearch for other works by this author on:B. Hernández;B. HernándezUCD Conway Institute, School of Medicine and Medical Science, University College DublinDublin 4IrelandSearch for other works by this author on:S. Ademowo;S. AdemowoUCD Conway Institute, School of Medicine and Medical Science, University College DublinDublin 4IrelandSearch for other works by this author on:M. Dharsee;M. DharseeOntario Cancer Biomarker NetworkTorontoOntarioM5A 2K3CanadaSearch for other works by this author on:K. Evans;K. EvansOntario Cancer Biomarker NetworkTorontoOntarioM5A 2K3CanadaSearch for other works by this author on:R. W. Watson;R. W. WatsonUCD Conway Institute, School of Medicine and Medical Science, University College DublinDublin 4IrelandSearch for other works by this author on:K. A. Tasken;K. A. TaskenDepartment of Tumor Biology, Institute for Cancer Research, Oslo University HospitalNorwaySearch for other works by this author on:S. R. PenningtonS. R. PenningtonUCD Conway Institute, School of Medicine and Medical Science, University College DublinDublin 4IrelandSearch for other works by this author on:
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CHAPTER 14: MRM-based Protein Quantification with Labeled Standards for Biomarker Discovery, Verification, and Validation in Human Plasmap316-328ByAndrew J. Percy;Andrew J. PercyUniversity of Victoria - Genome British Columbia Proteomics CentreVancouver Island Technology Park#3101–4464 Markham StreetVictoriaBC V8Z 7X8CanadaSearch for other works by this author on:Andrew G. Chambers;Andrew G. ChambersUniversity of Victoria - Genome British Columbia Proteomics CentreVancouver Island Technology Park#3101–4464 Markham StreetVictoriaBC V8Z 7X8CanadaSearch for other works by this author on:Carol E. Parker;Carol E. ParkerUniversity of Victoria - Genome British Columbia Proteomics CentreVancouver Island Technology Park#3101–4464 Markham StreetVictoriaBC V8Z 7X8CanadaSearch for other works by this author on:Christoph H. BorchersChristoph H. BorchersUniversity of Victoria - Genome British Columbia Proteomics CentreVancouver Island Technology Park#3101–4464 Markham StreetVictoriaBC V8Z 7X8CanadaDepartment of Biochemistry and Microbiology, University of VictoriaPetch Building Room 2073800 Finnerty RoadVictoriaBC V8P 5C2Canadachristoph@proteincentre.comSearch for other works by this author on:
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CHAPTER 15: Mass Spectrometry-based Quantification of Proteins and Peptides in Foodp329-348ByPhil E. Johnson;Phil E. JohnsonInstitute of Inflammation and Repair, Manchester Academic Health Science Centre, Manchester Institute of Biotechnology, University of ManchesterUKclare.mills@manchester.ac.ukSearch for other works by this author on:Justin T. Marsh;Justin T. MarshInstitute of Inflammation and Repair, Manchester Academic Health Science Centre, Manchester Institute of Biotechnology, University of ManchesterUKclare.mills@manchester.ac.ukSearch for other works by this author on:E. N. Clare MillsE. N. Clare MillsInstitute of Inflammation and Repair, Manchester Academic Health Science Centre, Manchester Institute of Biotechnology, University of ManchesterUKclare.mills@manchester.ac.ukSearch for other works by this author on:
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