The last few decades have seen the rise of widely-available proteomics tools. From new data acquisition
devices, such as MALDI-MS and 2DE to new database searching softwares, these new products have paved the way for
high throughput microbial proteomics (HTMP). These tools are enabling researchers to gain new insights into microbial
metabolism, and are opening up new areas of study, such as protein-protein interactions (interactomics) discovery.
Computer software is a key part of these emerging fields. This current review considers: 1) software tools for identifying
the proteome, such as MASCOT or PDQuest, 2) online databases of proteomes, such as SWISS-PROT, Proteome Web, or
the Proteomics Facility of the Pathogen Functional Genomics Resource Center, and 3) software tools for applying
proteomic data, such as PSI-BLAST or VESPA. These tools allow for research in network biology, protein identification,
functional annotation, target identification/validation, protein expression, protein structural analysis, metabolic pathway
engineering and drug discovery.