Mass Spectrometry Data Analysis in Proteomics

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 Mass spectrometry. Kudzai Mutenda and Rune Matthiesen 18. Useful MS programs freely available on the internet Commercial Programs Rune Matthiesen 19. Appendices