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

doi:10.1016/j.jprot.2011.06.008

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 journal › Article › peer-review

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.

Original language	English
Pages (from-to)	202-210
Journal	Journal of Proteomics
Volume	75
Issue number	1
DOIs	https://doi.org/10.1016/j.jprot.2011.06.008
Publication status	Published - 2011

Subject classification (UKÄ)

Cancer and Oncology
Medicinal Chemistry

Free keywords

prostate specific antigen
isoforms
MALDI LTQ Orbitrap XL
ESI-LTQ FT-ICR
Proteios software environment
kallikrein-2

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.jprot.2011.06.008

Cite this

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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.",

keywords = "prostate specific antigen, isoforms, MALDI LTQ Orbitrap XL, ESI-LTQ FT-ICR, Proteios software environment, kallikrein-2",

author = "{\'A}kos V{\'e}gv{\'a}ri and Melinda Rezeli and Jari H{\"a}kkinen and Carina Sihlbom and Elisabet Carlsohn and Johan Malm and Hans Lilja and Thomas Laurell and Gy{\"o}rgy Marko-Varga",

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doi = "10.1016/j.jprot.2011.06.008",

language = "English",

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pages = "202--210",

journal = "Journal of Proteomics",

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T1 - Bioinformatic strategies for unambiguous identification of prostate specific antigen in clinical samples

AU - Végvári, Ákos

AU - Rezeli, Melinda

AU - Häkkinen, Jari

AU - Sihlbom, Carina

AU - Carlsohn, Elisabet

AU - Malm, Johan

AU - Lilja, Hans

AU - Laurell, Thomas

AU - Marko-Varga, György

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

KW - prostate specific antigen

KW - isoforms

KW - MALDI LTQ Orbitrap XL

KW - ESI-LTQ FT-ICR

KW - Proteios software environment

KW - kallikrein-2

U2 - 10.1016/j.jprot.2011.06.008

DO - 10.1016/j.jprot.2011.06.008

M3 - Article

SN - 1874-3919

VL - 75

SP - 202

EP - 210

JO - Journal of Proteomics

JF - Journal of Proteomics

IS - 1

ER -

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

Abstract

Subject classification (UKÄ)

Free keywords

UN SDGs

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