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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00209805%3A_____%2F17%3A00077933" target="_blank" >RIV/00209805:_____/17:00077933 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/67985904:_____/17:00475939 RIV/00216224:14310/17:00095603

Výsledek na webu

<a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201600323" target="_blank" >https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201600323</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/pmic.201600323" target="_blank" >10.1002/pmic.201600323</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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 &quot;sequential window acquisition of all theoretical spectra&quot; (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 (R2&gt;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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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 &quot;sequential window acquisition of all theoretical spectra&quot; (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 (R2&gt;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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Proteomics

ISSN

1615-9853

e-ISSN

—

Svazek periodika

17

Číslo periodika v rámci svazku

5

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

6

Strana od-do

1600323

Kód UT WoS článku

000397390800006

EID výsledku v databázi Scopus

2-s2.0-85013414422