Elective affinities--bioinformatic analysis of proteomic mass spectrometry data.

Shotgun proteomic strategies based on the identification of proteolytic peptides by tandem mass spectrometry and sequence database searches have emerged as useful approaches for qualitative and quantitative measurement of proteins in large scale studies. Coincidentally, the automated analysis of the resulting mass spectrometry data has become increasingly challenging. Important steps in the analysis include the statistical validation of peptide and protein identifications, the extraction of quantitative information, and the interpretation of identified peptide and protein lists. This review discusses current informatics methods and software available to analyze shotgun proteomics data.