Mass Spectrometry Data Analysis in Proteomics is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (...
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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.
Essential reference for mass spectrometry (MS) in proteomics and glycomics Concise protocols for optimizing search parameters in MS search engines Practical guide to MS data analysis and bioinformatics Thorough review of available databases for proteomics researchers Includes supplementary material: sn.pub/extras Inhalt 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