Bioinformatic strategies for unambiguous identification of prostate specific antigen in clinical samples

► Isoforms of prostate specific antigen were identified and specified by high resolution mass spectrometry. ► A bioinformatic strategy was developed for optimized identification of different PSA forms. ► Both peptide mass fingerprinting of MALDI-MS and peptide sequencing MS/MS results were generated. ► The Proteios software environment was employed to combine multiple database search engines in an automated manner. ► This strategy provided improved sequence-based identification.