High-throughput proteomics studies generate large amounts of data. Biological interpretation of these large scale datasets is often challenging. Over the years, several computational tools have been developed to facilitate meaningful interpretation of large-scale proteomics data. In this chapter, we describe various analyses that can be performed and bioinformatics tools and resources that enable users to do the analyses. Many Web-based and stand-alone tools are relatively user-friendly and can be used by most biologists without significant assistance.
Keywords: Enrichment; FunRich; Gene ontology; NetPath; Pathways; Phosphoproteome; Post-translational modifications; Reactome.