title: Bioinformatic strategies for unambiguous identification of prostate specific antigen in clinical samples.
abstract: Prostate specific antigen (PSA), as a widely used clinical biomarker in prostate cancer diagnostics, exists in multiple molecular forms. However, all of these forms might not be recognized in a given sample by the standard immunoassays. Therefore, we have investigated PSA isoforms, separated by size, using mass spectrometric analyses. The objective of these developments was to identify and specify the various forms of PSA. To optimize successful identification of different PSA forms, we have developed a bioinformatic strategy, consisting of high resolution MALDI-MS PMF and sequencing MS/MS data searches. To improve sequence-based identification, the recently introduced Proteios software environment was employed, allowing the combination of multiple database search engines in an automated manner. We could unambiguously identify PSA in clinical samples by all detectable tryptic peptides, which were found to be common in several isoforms.
authors: Clinical Protein Science & Imaging, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden. akos.vegvari@elmat.lth.se
authors: Akos
authors: A
authors: Végvári
authors: Melinda
authors: M
authors: Rezeli
authors: Jari
authors: J
authors: Häkkinen
authors: Carina
authors: C
authors: Sihlbom
authors: Elisabet
authors: E
authors: Carlsohn
authors: Johan
authors: J
authors: Malm
authors: Hans
authors: H
authors: Lilja
authors: Thomas
authors: T
authors: Laurell
authors: György
authors: G
authors: Marko-Varga
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D017430:Prostate-Specific Antigen / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000378:metabolism / Q000473:pathology*; D020033:Protein Isoforms / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D012984:Software; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D014357:Trypsin / Q000378:metabolism
chemical_list: D010446:Peptide Fragments; D020033:Protein Isoforms; D014357:Trypsin; D017430:Prostate-Specific Antigen