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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.
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.