Mass Spectrometry Data Analysis in Proteomics / Edition 1

by Rune Matthiesen

Overview

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.

Product Details

ISBN-13:	9781588295637
Publisher:	Springer-Verlag New York, LLC
Publication date:	11/15/2006
Series:	Methods in Molecular Biology , #367
Edition description:	2007
Pages:	320
Product dimensions:	6.10(w) x 9.25(h) x 0.36(d)

Table of Contents

Preface     v
Contributors     ix
Introduction to Proteomics   Rune Matthiesen   Kudzai E. Mutenda     1
Extracting Monoisotopic Single-Charge Peaks From Liquid Chromatography-Electrospray Ionization-Mass Spectrometry   Rune Matthiesen     37
Calibration of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Peptide Mass Fingerprinting Spectra   Karin Hjerno   Peter Hojrup     49
Protein Identification by Peptide Mass Fingerprinting   Karin Hjerno     61
Generating Unigene Collections of Expressed Sequence Tag Sequences for Use in Mass Spectrometry Identification   Jeppe Emmersen     77
Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching   Alexey I. Nesvizhskii     87
Virtual Expert Mass Spectrometrist v3.0: An Integrated Tool for Proteome Analysis   Rune Matthiesen     121
Quantitation With Virtual Expert Mass Spectrometrist   Albrecht Gruhler   Rune Matthiesen     139
Sequence Handling by Sequence Analysis Toolbox v1.0   Christian Ravnsborg Ingrell   Rune Matthiesen   Ole Norregaard Jensen     153
Interpretation of Collision-Induced Fragmentation Tandem Mass Spectra of Posttranslationally Modified Peptides   JakobBunkenborg   Rune Matthiesen     169
Retention Time Prediction and Protein Identification   Magnus Palmblad     195
Quantitative Proteomics by Stable Isotope Labeling and Mass Spectrometry   Sheng Pan   Ruedi Aebersold     209
Quantitative Proteomics for Two-Dimensional Gels Using Difference Gel Electrophoresis   David B. Friedman     219
Proteomic Data Exchange and Storage: Using Proteios   Per Garden   Rikard Alm     241
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     261
Organization of Proteomics Data With YassDB   Allan L. Thomsen   Kris Laukens   Rune Matthiesen   Ole Nerregaard Jensen     271
Analysis of Carbohydrates by Mass Spectrometry   Kudzai E. Mutenda   Rune Matthiesen     289
Useful Mass Spectrometry Programs Freely Available on the Internet   Rune Matthiesen     303
Appendix     307
Index     313