Mass Spectrometry Data Analysis in Proteomics

Mass Spectrometry Data Analysis in Proteomics

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This is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. The 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.
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Product details

  • Hardback | 320 pages
  • 157.5 x 231.1 x 22.9mm | 657.72g
  • Humana Press Inc.
  • Totowa, NJ, United States
  • English
  • 2007 ed.
  • 17 Tables, black and white; 87 Illustrations, black and white; X, 320 p. 87 illus.
  • 158829563X
  • 9781588295637
  • 1,940,172

Table of contents

Mass Spectrometry Data Analysis in Proteomics

1. Introduction: Data types in proteomics.
Rune Matthiesen and Kudzai E. Mutenda

2. Extracting monoisotopic single charges peaks from LC-ESI-MS/MS data with VEMS.
Rune Matthiesen

3. Calibration of MALDI-TOF PMF spectra.
Karin Hjerno and Peter Hojrup

4. Protein identification by Peptide Mass Fingerprinting.
Karin Hjerno

5. Generating Unigene collections of EST sequences for use in MS identification
Jeppe Emmersen

6. Protein identification by tandem mass spectrometry and sequence database searching.
Alexey I. Nesvizhskii

7. VEMS an integrated tool for proteome analysis.
Rune Matthiesen

8. Quantitation with VEMS.
Albrecht Gruhler and Rune Matthiesen

9. Sequence handling by: Sequence Analysis Toolbox version 1.0
Christian Ravnsborg Rune Matthiesen Ole Norregaard Jensen

10. Interpretation of collision induced fragmentation tandem mass spectra of post-translationally modified peptides.
Jakob Bunkenborg and Rune Matthiesen

11. Retention time prediction and protein identification.
Magnus Palmblad

12. Quantitative Proteomics by Stable Isotope Labeling and Mass Spectrometry.
Sheng Pan

13. Quantitative Proteomics for Two-Dimensional Gels Using Difference Gel Electrophoresis (DIGE).
David B. Friedman, PhD, Mass Spectrometry

14. Proteomic Data Exchange and Storage - using Proteios
Per Garden and Rikard Alm

15. Proteomic Data Exchange and Storage - the Need for Common Standards and Public Repositories
Sandra Orchard, Philip Jones, Chris Taylor, Weimin Zhu, Randall K. Julian, Jr., Henning Hermjakob, Rolf Apweiler

16. Organisation of Proteomics Data
Allan L. Thomsen, Kris Laukens, Rune Matthiesen, Ole Norregaard Jensen

17. Analysis of carbohydrates by Massspectrometry.
Kudzai Mutenda and Rune Matthiesen

18. Useful MS programs freely available on the internet
Commercial Programs
Rune Matthiesen

19. Appendices
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