Mass spectrometry data analysis in proteomics

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Title:

Series:

Methods in molecular biology ; 367

Publication Information:

Totowa, NJ : Humana Press, 2006

ISBN:

9781588295637

Subject Term:

Proteomics -- Methodology

Mass spectrometry

Added Author:

Matthiesen, Rune

Available:*

Library	Item Barcode	Call Number	Material Type	Item Category 1	Status
Searching... PSZ JB	30000010164128	QP519.9.M3 M37 2007	Open Access Book	Book	Searching... Unknown

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.

Rune Matthiesen and Kudzai E. MutendaRune MatthiesenKarin Hjerno and Peter HojrupKarin HjernoJeppe EmmersenAlexey I. NesvizhskiiRune MatthiesenAlbrecht Gruhler and Rune MatthiesenChristian Ravnsborg Ingrell and Rune Matthiesen and Ole Norregaard JensenJakob Bunkenborg and Rune MatthiesenMagnus PalmbladSheng Pan and Ruedi AebersoldDavid B. FriedmanPer Garden and Rikard AlmSandra Orchard and Philip Jones and Chris Taylor and Weimin Zhu and Randall K. Julian, Jr. and Henning Hermjakob and Rolf ApweilerAllan L. Thomsen and Kris Laukens and Rune Matthiesen and Ole Nerregaard JensenKudzai E. Mutenda and Rune MatthiesenRune Matthiesen

Preface	p. v
Contributors	p. ix
1 Introduction to Proteomics	p. 1
2 Extracting Monoisotopic Single-Charge Peaks From Liquid Chromatography-Electrospray Ionization-Mass Spectrometry	p. 37
3 Calibration of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Peptide Mass Fingerprinting Spectra	p. 49
4 Protein Identification by Peptide Mass Fingerprinting	p. 61
5 Generating Unigene Collections of Expressed Sequence Tag Sequences for Use in Mass Spectrometry Identification	p. 77
6 Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching	p. 87
7 Virtual Expert Mass Spectrometrist v3.0: An Integrated Tool for Proteome Analysis	p. 121
8 Quantitation With Virtual Expert Mass Spectrometrist	p. 139
9 Sequence Handling by Sequence Analysis Toolbox v1.0	p. 153
10 Interpretation of Collision-Induced Fragmentation Tandem Mass Spectra of Posttranslationally Modified Peptides	p. 169
11 Retention Time Prediction and Protein Identification	p. 195
12 Quantitative Proteomics by Stable Isotope Labeling and Mass Spectrometry	p. 209
13 Quantitative Proteomics for Two-Dimensional Gels Using Difference Gel Electrophoresis	p. 219
14 Proteomic Data Exchange and Storage: Using Proteios	p. 241
15 Proteomic Data Exchange and Storage: The Need for Common Standards and Public Repositories	p. 261
16 Organization of Proteomics Data With YassDB	p. 271
17 Analysis of Carbohydrates by Mass Spectrometry	p. 289
18 Useful Mass Spectrometry Programs Freely Available on the Internet	p. 303
Appendix	p. 307
Index	p. 313

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