Proteome Bioinformatics

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 Labeling.- 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.