Mass Spectrometry Data Analysis in Proteomics
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Mass Spectrometry Data Analysis in Proteomics

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Rune Matthiesen
699 g
232x163x24 mm
367, Methods in Molecular Biology

Essential reference for mass spectrometry (MS) in proteomics and glycomics
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 Hjernø and Peter Højrup

4. Protein identification by Peptide Mass Fingerprinting.
Karin Hjernø

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 Nørregaard 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 Gärdén 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 Nørregaard 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
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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