Bioinformatics Resources for Interpreting Proteomics Mass Spectrometry Data.

Developments in mass spectrometry (MS) instrumentation have supported the advance of a variety of proteomic technologies that have enabled scientists to assess differences between healthy and diseased states. In particular, the ability to identify altered biological processes in a cell has led to the identification of novel drug targets, the development of more effective therapeutic drugs, and the growth of new diagnostic approaches and tools for personalized medicine applications. Nevertheless, large-scale proteomic data generated by modern mass spectrometers are extremely complex and necessitate equally complex bioinformatics tools and computational algorithms for their interpretation. A vast number of commercial and public resources have been developed for this purpose, often leaving the researcher perplexed at the overwhelming list of choices that exist. To address this challenge, the aim of this chapter is to provide a roadmap to the basic steps that are involved in mass spectrometry data acquisition and processing, and to describe the most common tools that are available for placing the results in biological context.