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.

Základní údaje

Originální název

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

Autoři

FAKTOR, Jakub (703 Slovensko), Rita SUCHÁ (203 Česká republika), Vendula PÁRALOVÁ (203 Česká republika, domácí), Yansheng LIU (156 Čína) a Pavel BOUCHAL (203 Česká republika, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10609 Biochemical research methods

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 3.532

Kód RIV

RIV/00216224:14310/17:00095603

Organizační jednotka

Přírodovědecká fakulta

DOI

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

UT WoS

000397390800006

Klíčová slova anglicky

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

Štítky

NZ, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 3. 2018 15:37, Ing. Nicole Zrilić

Anotace

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.

Návaznosti

GA17-05957S, projekt VaV

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

Investor: Grantová agentura ČR, Evaluace nových potenciálních cílů a inhibitorů pro blokování vývoje metastáz u luminálních A nádorů prsu

Citovat

FAKTOR, Jakub, Rita SUCHÁ, Vendula PÁRALOVÁ, Yansheng LIU a Pavel BOUCHAL. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. Proteomics. HOBOKEN, USA: Wiley, 2017, roč. 17, č. 5, s. nestránkováno, 6 s. ISSN 1615-9853. Dostupné z: 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 a Pavel BOUCHAL. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. \textit{Proteomics}. HOBOKEN, USA: Wiley, 2017, roč.~17, č.~5, s.~nestránkováno, 6 s. ISSN~1615-9853. Dostupné z: https://dx.doi.org/10.1002/pmic.201600323.

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