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.

Basic information

Original name

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

Authors

LAPČÍK, Petr (203 Czech Republic, belonging to the institution), Lucia JANÁČOVÁ (703 Slovakia, belonging to the institution), Pavla BOUCHALOVÁ (203 Czech Republic, belonging to the institution), David POTĚŠIL (203 Czech Republic, belonging to the institution), Ján PODHOREC (703 Slovakia, belonging to the institution), Milan HORA (203 Czech Republic), Alexandr POPRACH (203 Czech Republic, belonging to the institution), Ondřej FIALA (203 Czech Republic) and Pavel BOUCHAL (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10609 Biochemical research methods

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.400

RIV identification code

RIV/00216224:14310/22:00125181

Organization unit

Faculty of Science

DOI

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

UT WoS

000733225700001

Keywords in English

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

Abstract

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.

Links

LM2018127, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/A/1604/2020, interní kód MU

Name: Podpora biochemického výzkumu v roce 2021

Investor: Masaryk University

NV19-08-00250, research and development project

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

Investor: Ministry of Health of the CR

90127, large research infrastructures

Name: CIISB II

Citovat

LAPČÍK, Petr, Lucia JANÁČOVÁ, Pavla BOUCHALOVÁ, David POTĚŠIL, Ján PODHOREC, Milan HORA, Alexandr POPRACH, Ondřej FIALA and Pavel BOUCHAL. A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues. Proteomics. Weinheim: Wiley-VCH GmbH, 2022, vol. 22, No 7, p. "e2100228", 7 pp. ISSN 1615-9853. Available from: 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 and Pavel BOUCHAL. A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues. \textit{Proteomics}. Weinheim: Wiley-VCH GmbH, 2022, vol.~22, No~7, p.~''e2100228'', 7 pp. ISSN~1615-9853. Available from: https://dx.doi.org/10.1002/pmic.202100228.

Detailed Information on Publication Record