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Mass Spectrometry Data Analysis in Proteomics

  • Book
  • © 2013

Overview

Editors:
  1. Rune Matthiesen

    1. Inst. Molecular Pathology & Immunology, Universidade do Porto Inst. Molecular Pathology & Immunology, Porto, Portugal

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  • Collects cutting-edge methods and protocols involving mass spectrometry-based proteomics and relevant data analysis
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts to ensure successful results
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1007)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Introduction to Mass Spectrometry-Based Proteomics

    • Rune Matthiesen, Jakob Bunkenborg
    Pages 1-45

  3. LC-MS Spectra Processing

    • Rune Matthiesen
    Pages 47-63

  4. Isotopic Distributions

    • Alan L. Rockwood, Magnus Palmblad
    Pages 65-99

  5. Retention Time Prediction and Protein Identification

    • Alex A. Henneman, Magnus Palmblad
    Pages 101-118

  6. Algorithms for Database-Dependent Search of MS/MS Data

    • Rune Matthiesen
    Pages 119-138

  7. Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides

    • Jakob Bunkenborg, Rune Matthiesen
    Pages 139-171

  8. Improving Peptide Identification Using Empirical Scoring Systems

    • Robert J. Chalkley
    Pages 173-182

  9. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

    • Rune Matthiesen, Ana Sofia Carvalho
    Pages 183-217

  10. Computational Approaches to Selected Reaction Monitoring Assay Design

    • Conrad Bessant, Jun Fan
    Pages 219-235

  11. Feature Selection and Machine Learning with Mass Spectrometry Data

    • Susmita Datta
    Pages 237-262

  12. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data

    • Thomas E. Wales, Michael J. Eggertson, John R. Engen
    Pages 263-288

  13. Permethylated N-Glycan Analysis with Mass Spectrometry

    • Zhenxin Lin, David M. Lubman
    Pages 289-300

  14. Mass Spectrometry Methods for Studying Glycosylation in Cancer

    • Hugo Osório, Celso A. Reis
    Pages 301-316

  15. Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories

    • Rafael C. Jiménez, Juan Antonio Vizcaíno
    Pages 317-333

  16. Tools for Protein Posttranslational Modifications Analysis: FAK, a Case Study

    • Catarina Fonseca, Paula Voabil, Ana Sofia Carvalho, Rune Matthiesen
    Pages 335-358

  17. Proteomic Strategies to Characterize Signaling Pathways

    • H. C. Harsha, Sneha M. Pinto, Akhilesh Pandey
    Pages 359-377

  18. Simple Proteomics Data Analysis in the Object-Oriented PowerShell

    • Yassene Mohammed, Magnus Palmblad
    Pages 379-391

  19. Back Matter

    Pages 393-405
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Keywords

About this book

Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably.  Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics.  Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.

Editors and Affiliations

  • Inst. Molecular Pathology & Immunology, Universidade do Porto Inst. Molecular Pathology & Immunology, Porto, Portugal

    Rune Matthiesen

Bibliographic Information

  • Book Title: Mass Spectrometry Data Analysis in Proteomics

  • Editors: Rune Matthiesen

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-392-3

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2013

  • Hardcover ISBN: 978-1-62703-391-6Published: 11 May 2013

  • Softcover ISBN: 978-1-4939-5995-2Published: 23 August 2016

  • eBook ISBN: 978-1-62703-392-3Published: 13 May 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 405

  • Number of Illustrations: 34 b/w illustrations, 59 illustrations in colour

  • Topics: Protein Science, Mass Spectrometry

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