Mass Spectrometry Data Analysis in Proteomics

  • Rune Matthiesen

Part of the Methods in Molecular Biology book series (MIMB, volume 367)

Table of contents

  1. Front Matter
    Pages i-x
  2. Rune Matthiesen, Kudzai E. Mutenda
    Pages 1-35
  3. Rune Matthiesen
    Pages 121-138
  4. Albrecht Gruhler, Rune Matthiesen
    Pages 139-152
  5. Christian Ravnsborg Ingrell, Rune Matthiesen, Ole Nørregaard Jensen
    Pages 153-168
  6. Per Gärdén, Rikard Alm
    Pages 241-259
  7. Sandra Orchard, Philip Jones, Chris Taylor, Weimin Zhu, Randall K. Julian Jr., Henning Hermjakob et al.
    Pages 261-270
  8. Allan L. Thomsen, Kris Laukens, Rune Matthiesen, Ole Nørregaard Jensen
    Pages 271-287
  9. Kudzai E. Mutenda, Rune Matthiesen
    Pages 289-301
  10. Back Matter
    Pages 307-320

About this book


Mass Spectrometry Data Analysis in Proteomics is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. As MS is a high throughput technique, proteomic researchers must attend carefully to the associated field of data analysis, and this volume outlines available bioinformatics programs, algorithms, and databases available for MS data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with specific attention to identifying poor quality data and optimizing search parameters. Several different types of MS data are discussed, followed by a description of optimal methods for conversion of raw data into peak lists for input to search engines. Choosing the most accurate and complete databases is emphasized, and a report of available sequence databases is included. Methods for assembling expressed sequence tags (ESTs) into assembled nonredundant databases are provided, along with protocols for further processing the sequences into a format suitable for MS data. Mass Spectrometry Data Analysis in Proteomics describes publicly available applications whenever possible.


Mascot Proteomics Translation algorithms bioinformatics databases sequence analysis

Editors and affiliations

  • Rune Matthiesen
    • 1
  1. 1.Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark

Bibliographic information

  • DOI
  • Copyright Information Humana Press 2007
  • Publisher Name Humana Press
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-58829-563-7
  • Online ISBN 978-1-59745-275-5
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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