Proteome Bioinformatics - new book

The field of proteomics moves rapidly, as new methods, techniques, applications, standards, models and software appear almost on a daily basis. In Proteome Bioinformatics, 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. As a volume of the highly successful Methods in Molecular Biology series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Comprehensive and ground-breaking, Proteome Bioinformatics is an essential guidebook for the novice and expert alike, covering topics that address a wide range of data analysis and management problems. TOC:An Introduction to Proteome Bioinformatics.- Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting.- Computational approaches to peptide identification via tandem MS. Scoring and validation of tandem MS peptide identification methods.- Target-Decoy Search Strategy for Mass Spectrometry-based Proteomics.- Understanding and Exploiting Peptide Fragment Ion Intensities Using Experimental and Informatic Approaches.- Spectral Library Searching for Peptide Identification via Tandem MS.- De novo Sequencing Methods in Proteomics.- Cross Species Proteomics.- Gene model detection using mass spectrometry.- Signal Processing in Proteomics.- A High-Performance Reconfigurable Computing Solution for Peptide Mass Fingerprinting.- Mining proteomic MS/MS data for MRM transitions.- OpenMS and TOPP: Open Source Software for LC-MS Data Analysis.- Trans-Proteomic Pipeline: A Pipeline For Proteomic Analysis.- Informatics and statistics for analyzing 2-D gel electrophoresis images.- Automated generic analysis tools for protein quantitation using stable isotope labelling.- An overview of label-free quantitation methods in proteomics by mass spectrometry.- The PeptideAtlas Project.- Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis.- Molecular Interactions and data standardisation.- Mass Spectrometer Output File Format mzML.- Managing experimental data using FuGE.- Proteomics Data Collection (ProDaC).- Publishing and Collecting Proteomics Data Sets in Public Repositories using Standard Formats.- Computational Resources for the Prediction and Analysis of Native Disorder in Proteins.