PXD028411-2

PXD028411 is an original dataset announced via ProteomeXchange.

Title	A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues
Description	Generation 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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:53:37.655.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pavel Bouchal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 09:01:19	ID requested
1	2022-01-03 04:27:56	announced
⏵ 2	2023-11-14 08:53:38	announced	2023-11-14: Updated project metadata.
3	2024-10-22 05:30:46	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: data independent acquisition,Targeted proteomics, assay library, spectral library, renal cancer, selected reaction monitoring

Pavel Bouchal
contact affiliation	Masaryk University, Faculty of Science
contact email	bouchal@chemi.muni.cz
lab head
Pavel Bouchal
contact affiliation	Masaryk University, Faculty of Science
contact email	bouchal@chemi.muni.cz
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/01/PXD028411

PRIDE project URI

• PRIDE
  1. PXD028411
     1. Label: PRIDE project
     2. Name: A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues