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

Ákos Végvári, Melinda Rezeli, Jari Häkkinen, Carina Sihlbom, Elisabet Carlsohn, Johan Malm, Hans Lilja, Thomas Laurell, György Marko-Varga

Research output: Contribution to journalArticlepeer-review

2 Citations (SciVal)


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.
Original languageEnglish
Pages (from-to)202-210
JournalJournal of Proteomics
Issue number1
Publication statusPublished - 2011

Subject classification (UKÄ)

  • Cancer and Oncology
  • Medicinal Chemistry


  • prostate specific antigen
  • isoforms
  • MALDI LTQ Orbitrap XL
  • Proteios software environment
  • kallikrein-2


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