Proteome Bioinformatics

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  • Edition: 1st
  • Format: Hardcover
  • Copyright: 2010-01-23
  • Publisher: Humana Pr Inc

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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.

Table of Contents

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

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