Peptide Spectrum Matching
via Database Search and Spectral Library Search
Identification and Localization of Post-Translational Modifications by High-Resolution Mass Spectrometry
Algorithms for MS1-Based Quantitation
Informatics Solutions for Selected Reaction Monitoring
Data Analysis for Data Independent Acquisition
Data Formats of the Proteomics Standards Initiative
OpenMS: A Modular, Open-Source Workflow System for the Analysis of Quantitative Proteomics Data
Using Galaxy for Proteomics
Proteomics Informed by Transcriptomics
About this book
The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.
Conrad Bessant is Professor of Bioinformatics at Queen Mary University of London. He has particular interests in proteomics, software development and machine learning and is striving to ensure that everyone using proteomics data can access the latest analysis methods and knows how to use them in the most effective way.