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

a 2021

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

Název česky

Rozsáhlá knihovna cílených hmotnostně-spektrometrických assays pro kvantifikaci proteinů v tkáních renálního karcinomu

Autoři

LAPČÍK, Petr, Lucia JANÁČOVÁ, Pavla BOUCHALOVÁ, David POTĚŠIL, Ján PODHOREC, Milan HORA, Alexandr POPRACH, Ondřej FIALA a Pavel BOUCHAL

Vydání

20th Human Proteome Organization World Congress, HUPO Reconnect 2021, Online, 15.11.-19.11.2021, in Book of Abstracts, p. 184. 2021

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam

Změněno: 2. 11. 2024 20:37, Ing. Martina Blahová

Anotace

V originále

Introduction. Renal cell carcinoma (RCC) represents 2.2 % of cancer incidences, however, prognostic or predictive protein biomarkers specific for RCC are generally not available. 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. Methods. 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 and analyzed using LC-MS/MS on QExactive HF-X mass spectrometer in data-dependent acquisition mode. The library was generated in Spectronaut software. Two published datasets A-B [1] [2] and two new pilot datasets C-D of localized and metastatic RCC tissues measured in data-independent acquisition (DIA) mode were processed using the new library in Spectronaut. Results. The newly established assay library contains 77,817 peptides representing 7960 protein groups (FDR=1%). Its application resulted in increased numbers of quantified proteins in datasets A (2463 proteins, +4%) and B (4492 protein groups, >2 fold), with a clear separation of tumor and non-tumor tissues in both studies. Analysis of datasets C of metastatic RCC responding vs. non-responding to sunitinib treatment and dataset D of initially localized vs. metastatic RCC tissues led to consistent quantification of 5181 and 5253 protein groups (FDR=1%). Conclusions. Application of our spectral library leads to quantification of substantially increased part of RCC proteome. The new library has potential to contribute to better understanding the RCC development at molecular level, leading to new diagnostic and therapeutic targets.

Návaznosti

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. In 20th Human Proteome Organization World Congress, HUPO Reconnect 2021, Online, 15.11.-19.11.2021, in Book of Abstracts, p. 184. 2021.

@proceedings{1816739,
   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},
   booktitle = {20th Human Proteome Organization World Congress, HUPO Reconnect 2021, Online, 15.11.-19.11.2021, in Book of Abstracts, p. 184.},
   keywords = {assay library, data independent acquisition, mass spectrometry, proteomics, renal cell carcinoma},
   language = {eng},
   title = {A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues},
   url = {https://hupo2021.org/wp-content/uploads/2021/11/HUPO-2021-Abstract-Book_Oct-27.pdf},
   year = {2021}
}

TY  - CONF
ID  - 1816739
AU  - Lapčík, Petr - Janáčová, Lucia - Bouchalová, Pavla - Potěšil, David - Podhorec, Ján - Hora, Milan - Poprach, Alexandr - Fiala, Ondřej - Bouchal, Pavel
PY  - 2021
TI  - A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues
KW  - assay library, data independent acquisition, mass spectrometry, proteomics, renal cell carcinoma
UR  - https://hupo2021.org/wp-content/uploads/2021/11/HUPO-2021-Abstract-Book_Oct-27.pdf
N2  - Introduction. Renal cell carcinoma (RCC) represents 2.2 % of cancer incidences, however, prognostic or predictive protein biomarkers specific for RCC are generally not available. 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. Methods. 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 and analyzed using LC-MS/MS on QExactive HF-X mass spectrometer in data-dependent acquisition mode. The library was generated in Spectronaut software. Two published datasets A-B [1] [2] and two new pilot datasets C-D of localized and metastatic RCC tissues measured in data-independent acquisition (DIA) mode were processed using the new library in Spectronaut. Results. The newly established assay library contains 77,817 peptides representing 7960 protein groups (FDR=1%). Its application resulted in increased numbers of quantified proteins in datasets A (2463 proteins, +4%) and B (4492 protein groups, >2 fold), with a clear separation of tumor and non-tumor tissues in both studies. Analysis of datasets C of metastatic RCC responding vs. non-responding to sunitinib treatment and dataset D of initially localized vs. metastatic RCC tissues led to consistent quantification of 5181 and 5253 protein groups (FDR=1%). Conclusions. Application of our spectral library leads to quantification of substantially increased part of RCC proteome. The new 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. In \textit{20th Human Proteome Organization World Congress, HUPO Reconnect 2021, Online, 15.11.-19.11.2021, in Book of Abstracts, p. 184.}. 2021.

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