Proteome Bioinformatics

The field of proteomics moves rapidly, as new methods, techniques, applications, standards, models and software appear almost on a daily basis. In Proteome Bioinformatics: Methods and Protocols, expert researchers explore this ever-changing field, providing the reader with a mix of review and methodology chapters which address the fundamentals of analysis methods, algorithms, data standards and databases. Chapters include practical considerations for analyzing database search results, annotating genomes, speeding up searches, and responding to specific data processing challenges. Composed in the highly successful Methods in Molecular Biology'„¢ series format, chapters contain a brief introduction, include step-by-step methods and a list of necessary materials wherever possible, and share tips on troubleshooting and avoiding known pitfalls.Comprehensive and ground-breaking, Proteome Bioinformatics: Methods and Protocols is an essential guidebook for the novice and expert alike, as it covers topics that are crucial for addressing a wide range of data analysis and management problems.

Preface	p. v
Contributors	p. ix
An Introduction to Proteome Bioinformatics	p. 1
Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting	p. 7
Computational Approaches to Peptide Identification via Tandem MS	p. 23
Scoring and Validation of Tandem MS Peptide Identification Methods	p. 43
Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics	p. 55
Understanding and Exploiting Peptide Fragment Ion Intensities Using Experimental and Informatic Approaches	p. 73
Spectral Library Searching for Peptide Identification via Tandem MS	p. 95
De Novo Sequencing Methods in Proteomics	p. 105
Cross Species Proteomics	p. 123
Gene Model Detection Using Mass Spectrometry	p. 137
Signal Processing in Proteomics	p. 145
A High-Performance Reconfigurable Computing Solution for Peptide Mass Fingerprinting	p. 163
Mining Proteomic MS/MS Data for MRM Transitions	p. 187
OpenMS and TOPP: Open Source Software for LC-MS Data Analysis	p. 201
Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis	p. 213
Informatics and Statistics for Analyzing 2-D Gel Electrophoresis Images	p. 239
Automated Generic Analysis Tools for Protein Quantitation Using Stable Isotope Labeling	p. Ting-Yi Sung
An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry	p. 273
The PeptideAtlas Project	p. 285
Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis	p. 297
Molecular Interactions and Data Standardisation	p. 309
Mass Spectrometer Output File Format mzML	p. 319
Managing Experimental Data Using FuGE	p. 333
Proteomics Data Collection (ProDaC): Publishing and Collecting Proteomics Data Sets in Public Repositories Using Standard Formats	p. 345
Computational Resources for the Prediction and Analysis of Native Disorder in Proteins	p. 369
Index	p. 395
Table of Contents provided by Ingram. All Rights Reserved.

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Proteome Bioinformatics

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