A large-scale assay library for targeted protein quantification
in renal cell carcinoma tissues

J 2022

A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues

LAPČÍK, Petr, Lucia JANÁČOVÁ, Pavla BOUCHALOVÁ, David POTĚŠIL, Ján PODHOREC et. al.

Základní údaje

Originální název

A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues

Autoři

LAPČÍK, Petr (203 Česká republika, domácí), Lucia JANÁČOVÁ (703 Slovensko, domácí), Pavla BOUCHALOVÁ (203 Česká republika, domácí), David POTĚŠIL (203 Česká republika, domácí), Ján PODHOREC (703 Slovensko, domácí), Milan HORA (203 Česká republika), Alexandr POPRACH (203 Česká republika, domácí), Ondřej FIALA (203 Česká republika) a Pavel BOUCHAL (203 Česká republika, garant, domácí)

Vydání

Proteomics, Weinheim, Wiley-VCH GmbH, 2022, 1615-9853

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10609 Biochemical research methods

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.400

Kód RIV

RIV/00216224:14310/22:00125181

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1002/pmic.202100228

UT WoS

000733225700001

Klíčová slova anglicky

assay library; data independent acquisition; mass spectrometry; proteomics; renal cell carcinoma

Štítky

14110811, CF PROT, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 10. 10. 2024 14:09, Ing. Martina Blahová

Anotace

V originále

Renal cell carcinoma (RCC) represents 2.2% of all cancer incidences; however, prognostic or predictive RCC biomarkers at protein level are largely missing. To support proteomics research of localized and metastatic RCC, we introduce a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of 86 initially localized RCC, 75 metastatic RCC and 17 adjacent non-cancerous fresh frozen tissue lysates were trypsin digested, pooled, and fractionated using hydrophilic chromatography. The fractions were analyzed using LC-MS/MS on QExactive HF-X mass spectrometer in data-dependent acquisition (DDA) mode. A resulting spectral library contains 77,817 peptides representing 7960 protein groups (FDR = 1%). Further, we confirm applicability of this library on four RCC datasets measured in data-independent acquisition (DIA) mode, demonstrating a specific quantification of a substantially increased part of RCC proteome, depending on LC-MS/MS instrumentation. Impact of sample specificity of the library on the results of targeted DIA data extraction was demonstrated by parallel analyses of two datasets by two pan human libraries. The new RCC specific library has potential to contribute to better understanding the RCC development at molecular level, leading to new diagnostic and therapeutic targets.

Návaznosti

LM2018127, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii (Akronym: CIISB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech Infrastructure for Integrative Structural Biology

MUNI/A/1604/2020, interní kód MU

Název: Podpora biochemického výzkumu v roce 2021

Investor: Masarykova univerzita, Podpora biochemického výzkumu v roce 2021

NV19-08-00250, projekt VaV

Název: Proteotypová klasifikace renálního karcinomu ve vztahu k prognóze a terapeutické odpovědi

Investor: Ministerstvo zdravotnictví ČR, Proteotypová klasifikace renálního karcinomu ve vztahu k prognóze a terapeutické odpovědi

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

LAPČÍK, Petr, Lucia JANÁČOVÁ, Pavla BOUCHALOVÁ, David POTĚŠIL, Ján PODHOREC, Milan HORA, Alexandr POPRACH, Ondřej FIALA a Pavel BOUCHAL. A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues. Proteomics. Weinheim: Wiley-VCH GmbH, 2022, roč. 22, č. 7, s. "e2100228", 7 s. ISSN 1615-9853. Dostupné z: https://dx.doi.org/10.1002/pmic.202100228.

@article{1822322,
   author = {Lapčík, Petr and Janáčová, Lucia and Bouchalová, Pavla and Potěšil, David and Podhorec, Ján and Hora, Milan and Poprach, Alexandr and Fiala, Ondřej and Bouchal, Pavel},
   article_location = {Weinheim},
   article_number = {7},
   doi = {http://dx.doi.org/10.1002/pmic.202100228},
   keywords = {assay library; data independent acquisition; mass spectrometry; proteomics; renal cell carcinoma},
   language = {eng},
   issn = {1615-9853},
   journal = {Proteomics},
   title = {A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues},
   url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202100228},
   volume = {22},
   year = {2022}
}

TY  - JOUR
ID  - 1822322
AU  - Lapčík, Petr - Janáčová, Lucia - Bouchalová, Pavla - Potěšil, David - Podhorec, Ján - Hora, Milan - Poprach, Alexandr - Fiala, Ondřej - Bouchal, Pavel
PY  - 2022
TI  - A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues
JF  - Proteomics
VL  - 22
IS  - 7
SP  - "e2100228"
EP  - "e2100228"
PB  - Wiley-VCH GmbH
SN  - 16159853
KW  - assay library
KW  - data independent acquisition
KW  - mass spectrometry
KW  - proteomics
KW  - renal cell carcinoma
UR  - https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202100228
N2  - Renal cell carcinoma (RCC) represents 2.2% of all cancer incidences; however, prognostic or predictive RCC biomarkers at protein level are largely missing. To support proteomics research of localized and metastatic RCC, we introduce a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of 86 initially localized RCC, 75 metastatic RCC and 17 adjacent non-cancerous fresh frozen tissue lysates were trypsin digested, pooled, and fractionated using hydrophilic chromatography. The fractions were analyzed using LC-MS/MS on QExactive HF-X mass spectrometer in data-dependent acquisition (DDA) mode. A resulting spectral library contains 77,817 peptides representing 7960 protein groups (FDR = 1%). Further, we confirm applicability of this library on four RCC datasets measured in data-independent acquisition (DIA) mode, demonstrating a specific quantification of a substantially increased part of RCC proteome, depending on LC-MS/MS instrumentation. Impact of sample specificity of the library on the results of targeted DIA data extraction was demonstrated by parallel analyses of two datasets by two pan human libraries. The new RCC specific library has potential to contribute to better understanding the RCC development at molecular level, leading to new diagnostic and therapeutic targets.
ER  -

LAPČÍK, Petr, Lucia JANÁČOVÁ, Pavla BOUCHALOVÁ, David POTĚŠIL, Ján PODHOREC, Milan HORA, Alexandr POPRACH, Ondřej FIALA a Pavel BOUCHAL. A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues. \textit{Proteomics}. Weinheim: Wiley-VCH GmbH, 2022, roč.~22, č.~7, s.~''e2100228'', 7 s. ISSN~1615-9853. Dostupné z: https://dx.doi.org/10.1002/pmic.202100228.

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