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New Developments in Mass Spectrometry
Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide
Edited by
Robert Winkler
Robert Winkler
CINVESTAV Unidad Irapuato, Mexico
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Hardback ISBN:
978-1-78801-721-3
PDF ISBN:
978-1-78801-988-0
EPUB ISBN:
978-1-78801-990-3
Special Collection:
2020 ebook collection
No. of Pages:
430
Publication date:
16 Mar 2020
About this book
Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facilitates the direct interaction between users and developers and accelerates the implementation of new concepts and ideas. The first section of the book covers the basics of mass spectrometry, experimental strategies, data operations, the open-source philosophy, metabolomics, proteomics and statistics/ data mining. In the second section, active programmers and users describe available software packages. Included tutorials, datasets and code examples can be used for training and for building custom workflows. Finally, every reader is invited to participate in the open science movement.
Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide, The Royal Society of Chemistry, 2020.
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Digital access
$250.00
Print format
Processing Metabolomics and Proteomics Data with Open Software
$250.00
Table of contents
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CHAPTER 1: Introductionp1-25ByRobert WinklerRobert WinklerDepartment of Biochemistry and Biotechnology, Center for Research and Advanced Studies (CINVESTAV) IrapuatoKm. 9.6 Libramiento Norte Carr. Irapuato-León36824 IrapuatoGuanajuatoMexico[email protected]Mass Spectrometry Group, Max Planck Institute for Chemical EcologyHans-Knöll-Straße 807745 JenaGermanySearch for other works by this author on:
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CHAPTER 2: Mass Spectrometry Data Operations and Workflowsp26-40ByMagnus PalmbladMagnus PalmbladLeiden University Medical Center, Center for Proteomics and MetabolomicsPostzone P1-Q, P.O. Box 9600Leiden2300 RCThe Netherlands[email protected]Search for other works by this author on:
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CHAPTER 3: Metabolomicsp41-95ByDavid S. Wishart;David S. WishartDepartment of Computing Science, University of AlbertaEdmontonABCanada T6G 2E9Search for other works by this author on:Joanna Godzien;Joanna GodzienCentro de Excelencia en Metabolomica y Bioanalysis, Univesidad San PabloMadridSpainClinical Research Centre, Medical University of BialystokPolandSearch for other works by this author on:Alberto Gil-de-la-Fuente;Alberto Gil-de-la-FuenteCentro de Excelencia en Metabolomica y Bioanalysis, Univesidad San PabloMadridSpainSearch for other works by this author on:Abraham Otero;Abraham OteroCentro de Excelencia en Metabolomica y Bioanalysis, Univesidad San PabloMadridSpainSearch for other works by this author on:Coral BarbasCoral BarbasCentro de Excelencia en Metabolomica y Bioanalysis, Univesidad San PabloMadridSpainSearch for other works by this author on:
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CHAPTER 4: Proteomicsp96-119ByMarc VaudelMarc VaudelCenter for Diabetes Research, Department of Clinical Science, University of BergenNorway[email protected]Center for Medical Genetics and Molecular Medicine, Haukeland University HospitalBergenNorwaySearch for other works by this author on:
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CHAPTER 5: Statistics, Data Mining and Modeling1p120-200ByMiguel Reboiro-Jato;Miguel Reboiro-JatoDepartment of Computer Science, University of Vigo, ESEI, Campus As Lagoas32004 OurenseSpain[email protected]The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende36310 VigoSpainSING Research Group, Galicia Sur Health Research Institute (ISS Galicia Sur), SERGAS-UVIGOSpainSearch for other works by this author on:Daniel Glez-Peña;Daniel Glez-PeñaDepartment of Computer Science, University of Vigo, ESEI, Campus As Lagoas32004 OurenseSpain[email protected]The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende36310 VigoSpainSING Research Group, Galicia Sur Health Research Institute (ISS Galicia Sur), SERGAS-UVIGOSpainSearch for other works by this author on:Hugo López-FernándezHugo López-FernándezDepartment of Computer Science, University of Vigo, ESEI, Campus As Lagoas32004 OurenseSpain[email protected]The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende36310 VigoSpainSING Research Group, Galicia Sur Health Research Institute (ISS Galicia Sur), SERGAS-UVIGOSpainSearch for other works by this author on:
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CHAPTER 6: OpenMS and KNIME for Mass Spectrometry Data Processingp201-231ByOliver Alka;Oliver AlkaDepartment for Computer Science, Applied Bioinformatics, University of TübingenSand 1472076 TübingenGermanySearch for other works by this author on:Timo Sachsenberg;Timo SachsenbergDepartment for Computer Science, Applied Bioinformatics, University of TübingenSand 1472076 TübingenGermanySearch for other works by this author on:Leon Bichmann;Leon BichmannDepartment for Computer Science, Applied Bioinformatics, University of TübingenSand 1472076 TübingenGermanySearch for other works by this author on:Julianus Pfeuffer;Julianus PfeufferDepartment for Computer Science, Applied Bioinformatics, University of TübingenSand 1472076 TübingenGermanyDepartment for Computer Science, Algorithmic Bioinformatics, Freie Universität BerlinTakustr. 914195 BerlinGermanySearch for other works by this author on:Hendrik Weisser;Hendrik WeisserSTORM Therapeutics Limited, Moneta Building, Babraham Research CampusCambridge CB22 3ATUKSearch for other works by this author on:Samuel Wein;Samuel WeinEpigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania9th Floor, Smilow Center for Translational Research 3400 Civic Center BlvdPhiladelphiaPA 19104USASearch for other works by this author on:Eugen Netz;Eugen NetzBiomolecular Interactions, Max Planck Institute for Developmental BiologyMax-Planck-Ring 572076 TübingenGermanySearch for other works by this author on:Marc Rurik;Marc RurikDepartment for Computer Science, Applied Bioinformatics, University of TübingenSand 1472076 TübingenGermanySearch for other works by this author on:Oliver Kohlbacher;Oliver KohlbacherDepartment for Computer Science, Applied Bioinformatics, University of TübingenSand 1472076 TübingenGermanyBiomolecular Interactions, Max Planck Institute for Developmental BiologyMax-Planck-Ring 572076 TübingenGermanyInstitute for Translational Bioinformatics, University Hospital TübingenHoppe-Seyler-Str. 972076 TübingenGermanyInstitute for Biomedical Informatics, University of TübingenSand 1472076 TübingenGermanyQuantitative Biology Center, University of TübingenAuf der Morgenstelle 1072076 TübingenGermanySearch for other works by this author on:Hannes RöstHannes RöstDepartment of Molecular Genetics, University of TorontoTorontoCanadaDepartment of Computer Science, University of TorontoTorontoCanadaSearch for other works by this author on:
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CHAPTER 7: Metabolomics Data Analysis Using MZminep232-254ByTomáš Pluskal;Tomáš PluskalWhitehead Institute for Biomedical Research455 Main StreetCambridgeMA 02142USA[email protected][email protected]Search for other works by this author on:Ansgar Korf;Ansgar KorfUniversity of Münster, Institute of Inorganic and Analytical Chemistry, Department of Analytical ChemistryCorrensstraße 28/30Münster48149GermanySearch for other works by this author on:Aleksandr Smirnov;Aleksandr SmirnovUniversity of North Carolina at Charlotte, Department of Bioinformatics and Genomics9331 Robert D. Snyder RdCharlotteNC 28223USASearch for other works by this author on:Robin Schmid;Robin SchmidUniversity of Münster, Institute of Inorganic and Analytical Chemistry, Department of Analytical ChemistryCorrensstraße 28/30Münster48149GermanySearch for other works by this author on:Timothy R. Fallon;Timothy R. FallonWhitehead Institute for Biomedical Research455 Main StreetCambridgeMA 02142USA[email protected][email protected]Massachusetts Institute of Technology, Department of Biology77 Massachusetts AveCambridgeMA 02139USASearch for other works by this author on:Xiuxia Du;Xiuxia DuUniversity of North Carolina at Charlotte, Department of Bioinformatics and Genomics9331 Robert D. Snyder RdCharlotteNC 28223USASearch for other works by this author on:Jing-Ke WengJing-Ke WengWhitehead Institute for Biomedical Research455 Main StreetCambridgeMA 02142USA[email protected][email protected]Massachusetts Institute of Technology, Department of Biology77 Massachusetts AveCambridgeMA 02139USASearch for other works by this author on:
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CHAPTER 8: Pre-processing and Analysis of Metabolomics Data with XCMS/R and XCMS Online1p255-280ByLaila Pamela Partida-Martínez;Laila Pamela Partida-MartínezDepartment of Genetic Engineering, Center for Research and Advanced Studies (CINVESTAV) IrapuatoKm. 9.6 Libramiento Norte Carr. Irapuato-León36824 IrapuatoGuanajuatoMexicoSearch for other works by this author on:Robert WinklerRobert WinklerDepartment of Biochemistry and Biotechnology, Center for Research and Advanced Studies (CINVESTAV) IrapuatoKm. 9.6 Libramiento Norte Carr. Irapuato-León36824 IrapuatoGto.Mexico[email protected]Mass Spectrometry Group, Max Planck Institute for Chemical EcologyHans-Knöll-Straße 807745 JenaGermanySearch for other works by this author on:
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CHAPTER 9: Statistical Evaluation and Integration of Multi-omics Data with MetaboAnalystp281-301ByDavid S. WishartDavid S. WishartDepartment of Biological Sciences, University of AlbertaEdmontonABCanada T6G 2E8Search for other works by this author on:
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CHAPTER 10: Modular metaX Pipeline for Processing Untargeted Metabolomics Data1p302-314ByBo WenBo WenLester and Sue Smith Breast Center, Baylor College of MedicineHoustonTexas 77030USA[email protected]Department of Molecular and Human Genetics, Baylor College of MedicineHoustonTexas 77030USASearch for other works by this author on:
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CHAPTER 11: Metabolite Annotation With CEU Mass Mediatorp315-322ByAlberto Gil-de-la-Fuente;Alberto Gil-de-la-FuenteUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Campus MontepríncipeMadrid28668Spain[email protected]Universidad San Pablo-CEU, CEU Universities, Department of Information Technology, Escuela Politécnica Superior, Campus MontepríncipeMadrid28668SpainSearch for other works by this author on:Joanna Godzien;Joanna GodzienUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Campus MontepríncipeMadrid28668Spain[email protected]Clinical Research Centre, Medical University of BialystokBialystok15-001PolandSearch for other works by this author on:Abraham Otero;Abraham OteroUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Campus MontepríncipeMadrid28668Spain[email protected]Universidad San Pablo-CEU, CEU Universities, Department of Information Technology, Escuela Politécnica Superior, Campus MontepríncipeMadrid28668SpainSearch for other works by this author on:Coral BarbasCoral BarbasUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Campus MontepríncipeMadrid28668Spain[email protected]Search for other works by this author on:
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CHAPTER 12: Metabolite Annotation Using In Silico Generated Compounds: MINE and BioTransformerp323-332ByAlberto Gil-de-la-Fuente;Alberto Gil-de-la-FuenteUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de FarmaciaCampus MontepríncipeMadrid28668Spain[email protected]Universidad San Pablo-CEU, CEU Universities, Department of Information Technology, Escuela Politécnica SuperiorCampus MontepríncipeMadrid28668SpainClinical Research Centre, Medical University of BialystokBialystok15-001PolandSearch for other works by this author on:Joanna Godzien;Joanna GodzienUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de FarmaciaCampus MontepríncipeMadrid28668Spain[email protected]Clinical Research Centre, Medical University of BialystokBialystok15-001PolandSearch for other works by this author on:Abraham Otero;Abraham OteroUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de FarmaciaCampus MontepríncipeMadrid28668Spain[email protected]Universidad San Pablo-CEU, CEU Universities, Department of Information Technology, Escuela Politécnica SuperiorCampus MontepríncipeMadrid28668SpainClinical Research Centre, Medical University of BialystokBialystok15-001PolandSearch for other works by this author on:Coral BarbasCoral BarbasUniversidad San Pablo-CEU, CEU Universities, Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de FarmaciaCampus MontepríncipeMadrid28668Spain[email protected]Clinical Research Centre, Medical University of BialystokBialystok15-001PolandSearch for other works by this author on:
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CHAPTER 13: Trans-Proteomic Pipeline for the Identification, Validation, and Quantification of Proteins1p333-344ByRobert L. MoritzRobert L. MoritzSearch for other works by this author on:
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CHAPTER 14: Quantitative Proteomics Data Analysis with PANDA, LFAQ and PANDA-viewp345-370ByKaikun Xu;Kaikun XuState Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing)Life Science Park Road No. 38102206BeijingChina[email protected]Search for other works by this author on:Cheng ChangCheng ChangState Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing)Life Science Park Road No. 38102206BeijingChina[email protected]Search for other works by this author on:
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CHAPTER 15: Proteomic Workflows with R/ R Markdownp371-380ByMagnus Palmblad;Magnus PalmbladLeiden University Medical Center, Center for Proteomics and MetabolomicsPostzone P1-Q, P.O. Box 9600Leiden2300RCThe Netherlands[email protected]Search for other works by this author on:Cesaré Ovando-VázquezCesaré Ovando-VázquezCONACYT Centro Nacional de Supercómputo, Instituto Potosino de Investigación Científica y Tecnológica A. C.Camino a la presade San JoséSan Luis Potosí78216Mexico[email protected]Search for other works by this author on:
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CHAPTER 16: Python in Proteomicsp381-398ByHannes L. RöstHannes L. RöstSearch for other works by this author on:
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CHAPTER 17: Mass Spectrometry Development Kit (MSDK): a Java Library for Mass Spectrometry Data Processingp399-405ByTomáš Pluskal;Tomáš PluskalWhitehead Institute for Biomedical Research455 Main StreetCambridgeMA 02142USA[email protected][email protected]Search for other works by this author on:Nils Hoffmann;Nils HoffmannLeibniz-Institut für Analytische Wissenschaften – ISAS – e.V.Otto-Hahn-Straße 6b44227 DortmundGermanySearch for other works by this author on:Xiuxia Du;Xiuxia DuUniversity of North Carolina at Charlotte, Department of Bioinformatics and Genomics9331 Robert D. Snyder RdCharlotteNC 28223USASearch for other works by this author on:Jing-Ke WengJing-Ke WengWhitehead Institute for Biomedical Research455 Main StreetCambridgeMA 02142USA[email protected][email protected]Massachusetts Institute of Technology, Department of Biology77 Massachusetts AveCambridgeMA 02139USASearch for other works by this author on:
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CHAPTER 18: MASSyPup64: Linux Live System for Mass Spectrometry Data Processingp406-414ByRobert WinklerRobert WinklerDepartment of Biochemistry and Biotechnology, Center for Research and Advanced Studies (CINVESTAV) IrapuatoKm. 9.6 Libramiento Norte Carr. Irapuato-León36824 IrapuatoGto.Mexico[email protected]Mass Spectrometry Group, Max Planck Institute for Chemical EcologyHans-Knöll-Straße 807745 JenaGermanySearch for other works by this author on:
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CHAPTER 19: Cross-platform Software Development and Distribution with Bioconda and BioContainersp415-426ByOlivier Sallou;Olivier SallouInstitut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) – GenOuest Platform, Université de RennesRennesFranceSearch for other works by this author on:Björn A. GrüningBjörn A. GrüningBioinformatics Group, Department of Computer Science, University of FreiburgFreiburg79110GermanySearch for other works by this author on:
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CHAPTER 20: Concluding Remarks and Perspectivesp427-430ByRobert WinklerRobert WinklerDepartment of Biochemistry and Biotechnology, Center for Research and Advanced Studies (CINVESTAV) IrapuatoKm. 9.6 Libramiento Norte Carr. Irapuato-León36824 IrapuatoGto.Mexico[email protected]Mass Spectrometry Group, Max Planck Institute for Chemical EcologyHans-Knöll-Straße 807745 JenaGermanySearch for other works by this author on:
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