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New Developments in Mass Spectrometry
Proteome Informatics
Edited by
Conrad Bessant
Conrad Bessant
Queen Mary University of London, UK
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Hardback ISBN:
978-1-78262-428-8
PDF ISBN:
978-1-78262-673-2
EPUB ISBN:
978-1-78262-957-3
Special Collection:
2016 ebook collection
No. of Pages:
412
Publication date:
15 Nov 2016
About this book
The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.
Proteome Informatics, The Royal Society of Chemistry, 2016.
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Digital access
$251.00
Print format
Proteome Informatics
$251.00
Table of contents
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Chapter 1: Introduction to Proteome Informaticsp1-14ByConrad BessantConrad BessantSchool of Biological and Chemical Sciences, Queen Mary University of LondonE1 4NSUK[email protected]Search for other works by this author on:
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Chapter 2: De novo Peptide Sequencingp15-38ByBin MaBin MaSearch for other works by this author on:
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Chapter 3: Peptide Spectrum Matching via Database Search and Spectral Library Searchp39-68ByBrian Netzel;Brian NetzelDepartment of Laboratory Medicine and Pathology, Mayo ClinicRochesterMNUSASearch for other works by this author on:Surendra DasariSurendra DasariSearch for other works by this author on:
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Chapter 4: PSM Scoring and Validationp69-92ByJyoti S. ChoudharyJyoti S. ChoudharySearch for other works by this author on:
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Chapter 5: Protein Inference and Groupingp93-115ByAndrew R. JonesAndrew R. JonesSearch for other works by this author on:
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CHAPTER 6: Identification and Localization of Post-Translational Modifications by High-Resolution Mass Spectrometryp116-132ByRune Matthiesen;Rune MatthiesenComputational and Experimental Biology Group, CEDOC - CHRONIC DISEASES RESEARCH CENTER, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de LisboaCampo dos Mártires da Pátria, 1301169-056 LisboaPortugal[email protected]Search for other works by this author on:Ana Sofia CarvalhoAna Sofia CarvalhoComputational and Experimental Biology Group, CEDOC - CHRONIC DISEASES RESEARCH CENTER, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de LisboaCampo dos Mártires da Pátria, 1301169-056 LisboaPortugal[email protected]Search for other works by this author on:
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Chapter 7: Algorithms for MS1-Based Quantitationp133-154ByHanqing Liao;Hanqing LiaoUniversity of Liverpool, Department of Electrical Engineering and ElectronicsBrownlow Hill, LiverpoolL69 3GJUK[email protected]Search for other works by this author on:Alexander Phillips;Alexander PhillipsUniversity of Liverpool, Department of Electrical Engineering and ElectronicsBrownlow Hill, LiverpoolL69 3GJUK[email protected]Search for other works by this author on:Andris Jankevics;Andris JankevicsUniversity of Liverpool, Department of Electrical Engineering and ElectronicsBrownlow Hill, LiverpoolL69 3GJUK[email protected]Search for other works by this author on:Andrew W. DowseyAndrew W. DowseyUniversity of Liverpool, Department of Electrical Engineering and ElectronicsBrownlow Hill, LiverpoolL69 3GJUK[email protected]Search for other works by this author on:
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Chapter 8: MS2-Based Quantitationp155-177ByMarc VaudelMarc VaudelSearch for other works by this author on:
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Chapter 9: Informatics Solutions for Selected Reaction Monitoringp178-199ByBirgit Schilling;Birgit SchillingBuck Institute for Research on Aging8001 Redwood BlvdNovatoCalifornia 94945USASearch for other works by this author on:Brendan Maclean;Brendan MacleanDepartment of Genome Sciences, University of Washington School of MedicineFoege Building S113, 3720 15th Ave NESeattleWashington 98195USASearch for other works by this author on:Jason M. Held;Jason M. HeldDepartments of Medicine and Anesthesiology, Washington University School of Medicine660 South Euclid AvenueSt. LouisMissouri 63110USASearch for other works by this author on:Bradford W. GibsonBradford W. GibsonBuck Institute for Research on Aging8001 Redwood BlvdNovatoCalifornia 94945USADepartment of Pharmaceutical Chemistry, University of CaliforniaSan FranciscoCA 94143USA[email protected]Search for other works by this author on:
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Chapter 10: Data Analysis for Data Independent Acquisitionp200-228ByPedro Navarro;Pedro NavarroInstitute for Immunology, University Medical Centre of the Johannes Gutenberg University Mainz55131 MainzGermany[email protected]Search for other works by this author on:Marco Trevisan-Herraz;Marco Trevisan-HerrazCentro Nacional de Investigaciones Cardiovasculares28029 MadridSpainSearch for other works by this author on:Hannes L. RöstHannes L. RöstDepartment of Genetics, Stanford UniversityStanfordCA 94305USASearch for other works by this author on:
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Chapter 11: Data Formats of the Proteomics Standards Initiativep229-258ByJuan Antonio Vizcaíno;Juan Antonio VizcaínoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome CampusHinxton, CambridgeCB10 1SDUK[email protected]Search for other works by this author on:Simon Perkins;Simon PerkinsInstitute of Integrative Biology, University of LiverpoolUKSearch for other works by this author on:Andrew R. Jones;Andrew R. JonesInstitute of Integrative Biology, University of LiverpoolUKSearch for other works by this author on:Eric W. DeutschEric W. DeutschInstitute for Systems Biology401 Terry Ave NSeattleWA 98109USASearch for other works by this author on:
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Chapter 12: OpenMS: A Modular, Open-Source Workflow System for the Analysis of Quantitative Proteomics Datap259-288ByLars NilseLars NilseInstitute of Molecular Medicine and Cell Research, University of FreiburgD-79104 FreiburgGermany[email protected]Search for other works by this author on:
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Chapter 13: Using Galaxy for Proteomicsp289-320ByCandace R. Guerrero;Candace R. GuerreroDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota321 Church St SE/6-155 Jackson HallMinneapolisMN 55455USA[email protected]Search for other works by this author on:Pratik D. Jagtap;Pratik D. JagtapDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota321 Church St SE/6-155 Jackson HallMinneapolisMN 55455USA[email protected]Center for Mass Spectrometry and Proteomics, University of Minnesota1479 Gortner Avenue, St. PaulMN 55108USASearch for other works by this author on:James E. Johnson;James E. JohnsonMinnesota Supercomputing Institute, University of Minnesota512 Walter Library, 117 Pleasant Street SEMinneapolisMN 55455USASearch for other works by this author on:Timothy J. GriffinTimothy J. GriffinDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota321 Church St SE/6-155 Jackson HallMinneapolisMN 55455USA[email protected]Center for Mass Spectrometry and Proteomics, University of Minnesota1479 Gortner Avenue, St. PaulMN 55108USASearch for other works by this author on:
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Chapter 14: R for Proteomicsp321-364ByLisa M. Breckels;Lisa M. BreckelsComputational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of CambridgeTennis Court RoadCambridgeCB2 1GAUK[email protected]Search for other works by this author on:Sebastian Gibb;Sebastian GibbDepartment of Anesthesiology and Intensive Care, University Medicine GreifswaldFerdinand-Sauerbruch-Straße17475 GreifswaldGermanySearch for other works by this author on:Vladislav Petyuk;Vladislav PetyukEarth and Biological Sciences Directorate, Pacific Northwest National LaboratoryRichlandWA 99352USASearch for other works by this author on:Laurent GattoLaurent GattoComputational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of CambridgeTennis Court RoadCambridgeCB2 1GAUK[email protected]Search for other works by this author on:
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Chapter 15: Proteogenomics: Proteomics for Genome Annotationp365-384ByFawaz Ghali;Fawaz GhaliInstitute of Integrative Biology, University of Liverpool, Biosciences Building Crown StreetLiverpoolL69 7ZBUK[email protected]School of Computing, Mathematics and Digital Technology, Manchester Metropolitan University, Chester StreetManchesterM1 5GDUKSearch for other works by this author on:Andrew R. JonesAndrew R. JonesInstitute of Integrative Biology, University of Liverpool, Biosciences Building Crown StreetLiverpoolL69 7ZBUK[email protected]Search for other works by this author on:
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Chapter 16: Proteomics Informed by Transcriptomicsp385-405ByShyamasree Saha;Shyamasree SahaSchool of Biological and Chemical Sciences, Queen Mary, University of LondonE1 4NSUK[email protected]Search for other works by this author on:David Matthews;David MatthewsSchool of Cellular and Molecular Medicine, University of Bristol, University WalkBristolBS8 1TDUKSearch for other works by this author on:Conrad BessantConrad BessantSchool of Biological and Chemical Sciences, Queen Mary, University of LondonE1 4NSUK[email protected]Search for other works by this author on:
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