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Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues
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SYSNO ASEP 0475939 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues Author(s) Faktor, J. (CZ)
Suchá, Rita (UZFG-Y) ORCID
Páralová, V. (CZ)
Liu, Y. (CH)
Bouchal, P. (CZ)Article number 1600323 Source Title Proteomics. - : Wiley - ISSN 1615-9853
Roč. 17, č. 5 (2017)Number of pages 6 s. Publication form Print - P Language eng - English Country DE - Germany Keywords cancer ; MRM/SRM ; SWATH Subject RIV EI - Biotechnology ; Bionics OECD category Technologies involving identifying the functioning of DNA, proteins and enzymes and how they influence the onset of disease and maintenance of well-being (gene-based diagnostics and therapeutic interventions (pharmacogenomics, gene-based therapeutics) R&D Projects LO1609 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Institutional support UZFG-Y - RVO:67985904 UT WOS 000397390800006 EID SCOPUS 85013414422 DOI 10.1002/pmic.201600323 Annotation Targeted mass spectrometry-based proteomics approaches enable the simultaneous and reproducible quantification of multiple protein analytes across numerous conditions in biology and clinical studies. These approaches involve e.g. selected reaction monitoring (SRM) typically conducted on a triple quadrupole mass spectrometer, its high-resolution variant named pseudo-SRM (p-SRM), carried out in a quadrupole coupled with an TOF analyzer (qTOF), and sequential window acquisition of all theoretical spektra (SWATH). Here we compared these methods in terms of signal-to-noise ratio (S/N), coefficient of variance (CV), fold change (FC), limit of detection and quantitation (LOD, LOQ). We have shown the highest S/N for p-SRM mode, followed by SRM and SWATH, demonstrating a trade-off between sensitivity and level of multiplexing for SRM, p-SRM, and SWATH. SRM was more sensitive than p-SRM based on determining their LOD and LOQ. Although SWATH has the worst S/N, it enables peptidemultiplexing with post-acquisition definition of the targets, leading to better proteome coverage. FC between breast tumors of different clinical-pathological characteristics were highly correlated (R-2>0.97) across three methods and consistent with the previous study on 96 tumor tissues. Our technical note presented here, therefore, confirmed that outputs of all the three methods were biologically relevant and highly applicable to cancer research. Workplace Institute of Animal Physiology and Genetics Contact Jana Zásmětová, knihovna@iapg.cas.cz, Tel.: 315 639 554 Year of Publishing 2018
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