Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues

0475939 - ÚŽFG 2018 RIV DE eng J - Journal Article
Faktor, J. - Suchá, Rita - Páralová, V. - Liu, Y. - Bouchal, P.
Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues.
Proteomics. Roč. 17, č. 5 (2017), č. článku 1600323. ISSN 1615-9853. E-ISSN 1615-9861
R&D Projects: GA MŠMT(CZ) LO1609
Institutional support: RVO:67985904
Keywords : cancer * MRM/SRM * SWATH
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)
Impact factor: 3.532, year: 2017

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.
Permanent Link: http://hdl.handle.net/11104/0272528