Dataset Information

CPTAC CCRCC Discovery Study - DIA Proteome

ABSTRACT: This is a supplementary study to the CPTAC CCRCC Discovery Study - Proteome. Unlabeled, digested peptide material from individual tissue samples (ccRCC and NAT) was spiked with index Retention Time (iRT) peptides (Biognosys) and subjected to data-independent acquisition (DIA) analysis. Kidney cancer is among the 10 most common cancers in both men and women and each year there are approximately 60,000 new cases with over 14,000 deaths (NCI, Surveillance, Epidemiology and End Results (SEER) Program). Several histological and molecular subtypes have been identified and clear cell renal cell carcinoma (CCRCC) is the most prevalent (Hsieh el al., 2017 Nat Rev Dis Primers). To advance the proteogenomic understanding of CCRCC, the CPTAC program has investigated 110 tumors (CPTAC discovery cohort) and subjected these samples to global proteome and phosphoproteome analysis. An optimized workflow for mass spectrometry of tissues using isobaric tags (TMT (tandem mass tags)-10) was used (Mertins et al., Nature Protocols 2018). Proteome and phosphoproteome data from the CCRCC tumors is available below along with peptide spectrum analyses (PSMs) and protein summary reports from the CPTAC common data analysis pipeline (CDAP). Clinical data is provided. Additional attributes along with genotypes will be available as cohort characterization proceeds. Genomic data will be available from the NCI Genomic Data Commons. Note: Sample-wise assessment of genomic profiles in this cohort identified seven tumor samples with molecular aberrations atypical for ccRCC. While these seven non-ccRCC samples (C3L-00359-01, C3N-00313-03, C3N-00435-05, C3N-00492-04, C3N-00832-01, C3N-01175-01, C3N-01180-01) and their corresponding NATs (C3N-00435-06, C3N-00492-05, C3N-01175-05) were excluded from the ccRCC cohort in all downstream analyses, the non-ccRCC samples served as useful controls to highlight ccRCC-specific features. These seven samples were therefore annotated as non-ccRCC samples.

Dataset imported into MassIVE from https://pdc.cancer.gov/pdc/study/PDC000200 on 10/04/23

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Hui Zhang

PROVIDER: MSV000093041 | MassIVE | Wed Oct 04 16:00:00 BST 2023

REPOSITORIES: MassIVE

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Publications

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.

Clark David J DJ Dhanasekaran Saravana M SM Petralia Francesca F Pan Jianbo J Song Xiaoyu X Hu Yingwei Y da Veiga Leprevost Felipe F Reva Boris B Lih Tung-Shing M TM Chang Hui-Yin HY Ma Weiping W Huang Chen C Ricketts Christopher J CJ Chen Lijun L Krek Azra A Li Yize Y Rykunov Dmitry D Li Qing Kay QK Chen Lin S LS Ozbek Umut U Vasaikar Suhas S Wu Yige Y Yoo Seungyeul S Chowdhury Shrabanti S Wyczalkowski Matthew A MA Ji Jiayi J Schnaubelt Michael M Kong Andy A Sethuraman Sunantha S Avtonomov Dmitry M DM Ao Minghui M Colaprico Antonio A Cao Song S Cho Kyung-Cho KC Kalayci Selim S Ma Shiyong S Liu Wenke W Ruggles Kelly K Calinawan Anna A Gümüş Zeynep H ZH Geiszler Daniel D Kawaler Emily E Teo Guo Ci GC Wen Bo B Zhang Yuping Y Keegan Sarah S Li Kai K Chen Feng F Edwards Nathan N Pierorazio Phillip M PM Chen Xi Steven XS Pavlovich Christian P CP Hakimi A Ari AA Brominski Gabriel G Hsieh James J JJ Antczak Andrzej A Omelchenko Tatiana T Lubinski Jan J Wiznerowicz Maciej M Linehan W Marston WM Kinsinger Christopher R CR Thiagarajan Mathangi M Boja Emily S ES Mesri Mehdi M Hiltke Tara T Robles Ana I AI Rodriguez Henry H Qian Jiang J Fenyö David D Zhang Bing B Ding Li L Schadt Eric E Chinnaiyan Arul M AM Zhang Zhen Z Omenn Gilbert S GS Cieslik Marcin M Chan Daniel W DW Nesvizhskii Alexey I AI Wang Pei P Zhang Hui H

Cell 20191001 4

To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genom ...[more]

PMID: 31675502

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