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

J 2017

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

FAKTOR, Jakub, Rita SUCHÁ, Vendula PÁRALOVÁ, Yansheng LIU, Pavel BOUCHAL et. al.

Basic information

Original name

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

Authors

FAKTOR, Jakub (703 Slovakia), Rita SUCHÁ (203 Czech Republic), Vendula PÁRALOVÁ (203 Czech Republic, belonging to the institution), Yansheng LIU (156 China) and Pavel BOUCHAL (203 Czech Republic, belonging to the institution)

Edition

Proteomics, HOBOKEN, USA, Wiley, 2017, 1615-9853

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10609 Biochemical research methods

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 3.532

RIV identification code

RIV/00216224:14310/17:00095603

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1002/pmic.201600323

UT WoS

000397390800006

Keywords in English

Cancer; MRM; SRM; p-SRM; SWATH; Tissue

Abstract

V originále

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 spectra" (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.

Links

GA17-05957S, research and development project

Name: Evaluace nových potenciálních cílů a inhibitorů pro blokování vývoje metastáz u luminálních A nádorů prsu

Investor: Czech Science Foundation

Citovat

FAKTOR, Jakub, Rita SUCHÁ, Vendula PÁRALOVÁ, Yansheng LIU and Pavel BOUCHAL. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. Proteomics. HOBOKEN, USA: Wiley, 2017, vol. 17, No 5, p. nestránkováno, 6 pp. ISSN 1615-9853. Available from: https://dx.doi.org/10.1002/pmic.201600323.

@article{1412657,
   author = {Faktor, Jakub and Suchá, Rita and Páralová, Vendula and Liu, Yansheng and Bouchal, Pavel},
   article_location = {HOBOKEN, USA},
   article_number = {5},
   doi = {http://dx.doi.org/10.1002/pmic.201600323},
   keywords = {Cancer; MRM; SRM; p-SRM; SWATH; Tissue},
   language = {eng},
   issn = {1615-9853},
   journal = {Proteomics},
   title = {Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues},
   volume = {17},
   year = {2017}
}

TY  - JOUR
ID  - 1412657
AU  - Faktor, Jakub - Suchá, Rita - Páralová, Vendula - Liu, Yansheng - Bouchal, Pavel
PY  - 2017
TI  - Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues
JF  - Proteomics
VL  - 17
IS  - 5
SP  - nestránkováno
EP  - nestránkováno
PB  - Wiley
SN  - 16159853
KW  - Cancer
KW  - MRM
KW  - SRM
KW  - p-SRM
KW  - SWATH
KW  - Tissue
N2  - 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 spectra" (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.
ER  -

FAKTOR, Jakub, Rita SUCHÁ, Vendula PÁRALOVÁ, Yansheng LIU and Pavel BOUCHAL. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. \textit{Proteomics}. HOBOKEN, USA: Wiley, 2017, vol.~17, No~5, p.~nestránkováno, 6 pp. ISSN~1615-9853. Available from: https://dx.doi.org/10.1002/pmic.201600323.

Detailed Information on Publication Record