Data management in mass spectrometry-based proteomics.

Mass spectrometry-based proteomics has made the transition from the analysis of a single or only a few proteins per experiment to a high-throughput platform for discovery/validation that can analyze several hundreds to thousands of proteins in a single experiment. This increase in analytical capability hinged on four main components: (1) innovative methodologies, (2) improved instruments, (3) ready availability of comprehensive protein sequence databases, and (4) development of sophisticated software algorithms to match fragmentation mass spectra against these databases. But as the throughput of the approach increased, so did the necessity to manage and automate the data processing workflow. Indeed, modern instruments generate tens of thousands of fragmentation spectra per hour, providing a substantial bioinformatics challenge. This chapter provides insight into the specifics of this challenge, by looking at a typical workflow, the data types and user roles involved, and a broad overview of available software solutions. Finally, the increasingly important link between a local data management system and the global, centralized dissemination of proteomics data is discussed.