BioWorks 3.2 enables scientists conducting protein or proteomics research to identify proteins. The program supports the range of Finnigan ion trap mass spectrometers, and finds applications in the pharmaceutical industry, academia, governmental laboratories, biotechnology companies and contract research organizations (CROs). It utilizes the SEQUEST algorithm for searching protein databases, and features probability-based scoring to complement traditional SEQUEST scores. This software automatically identifies proteins by comparing experimental tandem mass spectrometry (MS/MS) data with standard protein and DNA databases. The application can automatically analyze a single spectrum or an entire LC/MS/MS peptide map. Moreover, the algorithm can extract information and correctly identify proteins even at low concentrations that generate a weak signal.