Proteome Bioinformatics

This book probes the fluid field of proteomics, offering review and methodology chapters that address the fundamentals of analysis methods, algorithms, data standards and databases. Topics covered include a wide range of data analysis and management problems.

The feld of proteomics moves rapidly. New methods, techniques, applications, standards, models and software appear almost on a daily basis. Accompanying this are plenty of texts on the experimental side of the feld and a few appearing on the informatic and data analysis side. This latterly includes one in the Methods in Molecular Biology series tackling the specifc analysis of Mass spectrometry data in proteomics in MMB vol. 376. This current collection builds on this, but takes a broader view of proteome data analysis covering data analysis essentials, but also the databases and data models, as well as practical consid- ations for analysing database search results, annotating genomes, and speeding up searches. It also digs deeper into some topics, such as decoy database searching and aspects of signal processing in proteomic mass spectrometry. The aim of the volume is to provide the reader with a mix of reviews and methodology chapters, which build from the essentials of database searching in proteomics, on through specifc data processing challenges to databases, data standards and data models.

Includes cutting-edge informatics methods for identifying and quantifying proteins Provides descriptions of the main proteomics databases and guidance on proteomic data standards Gives an overview of statistics and scoring methods used in proteomics software Includes supplementary material: sn.pub/extras

Klappentext

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.

Inhalt
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.