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PXD028411 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA large-scale assay library for targeted protein quantification in renal cell carcinoma tissues
DescriptionGeneration of a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of primary tumor tissue lysates from 86 patients with initially localized renal cell carcinoma (RCC), 75 patients with metastatic RCC treated with sunitinib or pazopanib in the first line and 17 adjacent normal tissues treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic, or University Hospital Pilsen (UHP), Czech Republic, were used to generate the spectral library. Two previously published datasets (dataset A and B) and two newly generated RCC datasets (dataset C and D) were analyzed using the newly generated library showing increased number of quantified peptides and proteins, depending on the size of the library and LC-MS/MS instrumentation. This PRIDE project also includes quantitative analysis results for all four datasets and raw files for dataset C and D. Dataset A is characterized in DOI: 10.1038/nm.3807. It consists of 18 samples from 9 RCC patients involving one cancer and non-cancerous sample per patient. Dataset B is characterized in DOI: 10.3390/biomedicines9091145. It consists of 16 tumor samples and 16 adjacent normal tissues from 16 mRCC patients treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic. Dataset C involves only tumor tissues from dataset B. Half of them responded to sunitinib treatment in the first line three months after treatment initiation and half did not. Dataset D involves 16 RCC patients treated at University Hospital Pilsen (UHP), Czech Republic. All were localized at the time of initial diagnosis, half of the tumors developed distant metastasis in five years after the diagnosis.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterPavel Bouchal
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmethylthiolated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-09-09 09:01:19ID requested
12022-01-03 04:27:56announced
22023-11-14 08:53:38announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: data independent acquisition,Targeted proteomics, assay library, spectral library, renal cancer, selected reaction monitoring
Contact List
Pavel Bouchal
contact affiliationMasaryk University, Faculty of Science
contact emailbouchal@chemi.muni.cz
lab head
Pavel Bouchal
contact affiliationMasaryk University, Faculty of Science
contact emailbouchal@chemi.muni.cz
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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