MassIVE MSV000093041

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CPTAC CCRCC Discovery Study - DIA Proteome

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Description

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.

[doi:10.25345/C52V2CM61] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: CPTAC

Contact

Principal Investigators:
(in alphabetical order) 		Hui Zhang, Associate Prosfessor, Johns Hopkins University, Department of Pathology Baltimore USA, N/A
Submitting User: cptac

Publications

Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümü? ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H, Clinical Proteomic Tumor Analysis Consortium.
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.
Cell. 2019 Oct 31;179(4):964-983.e31.

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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.