Bioinformatic strategies for unambiguous identification of prostate specific antigen in clinical samples Journal Article
| Authors: | Végvári, T.; Rezeli, M.; Häkkinen, J.; Sihlbom, C.; Carlsohn, E.; Malm, J.; Lilja, H.; Laurell, T.; Marko-Varga, G. |
| Article 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. © 2011 Elsevier B.V. |
| Keywords: | controlled study; molecular genetics; methodology; mass spectrometry; prostate specific antigen; metabolism; biology; computational biology; pathology; data base; prostate-specific antigen; prostatic neoplasms; chemistry; amino acid sequence; molecular sequence data; antigen detection; prostate tumor; peptide fragments; peptide fragment; tandem mass spectrometry; matrix assisted laser desorption ionization time of flight mass spectrometry; computer program; software; isoprotein; protein isoforms; trypsin; spectrometry, mass, matrix-assisted laser desorption-ionization; search engine; maldi ltq orbitrap xl; kallikrein-2; esi-ltq ft-icr; prostate specific antigen isoforms; proteios software environment |
| Journal Title: | Journal of Proteomics |
| Volume: | 75 |
| Issue: | 1 |
| ISSN: | 1874-3919 |
| Publisher: | Elsevier Science BV |
| Date Published: | 2011-12-10 |
| Start Page: | 202 |
| End Page: | 210 |
| Language: | English |
| PROVIDER: | scopus |
| PMCID: | PMC3220806 |
| PUBMED: | 21723425 |
| DOI: | 10.1016/j.jprot.2011.06.008 |
| DOI/URL: | |
| Notes: | --- - Cited By (since 1996):1 - "Export Date: 7 May 2013" - ":doi 10.1016/j.jprot.2011.06.008" - ": Chemicals/CAStrypsin, 9002-07-7; Peptide Fragments; Prostate-Specific Antigen, 3.4.21.77; Protein Isoforms; Trypsin, 3.4.21.4" - "Source: Scopus" |
