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PXD013455

PXD013455 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleThe landscape of protein expression in cancer based on public proteomics data
DescriptionThis project contains raw data, intermediate files and results used to create the integrated map of protein expression in human cancer (including data from cell lines and tumours). The map is based on joint reanalysis of 11 large-scale quantitative proteomics studies. The datasets were primarily retrieved from the PRIDE database, as well as MassIVE database and CPTAC data portal. The raw files were manually curated in order to capture mass spectrometry acquisition parameters, experimental design and sample characteristics. The raw files were jointly processed with MaxQuant computational platform using standard settings (see Data Processing Protocol). Due to size of the data, the processing was done in two batches denoted as “celllines” and “tumours” analysis. In total, using a 1% peptide spectrum match and protein false discovery rates, the analysis allowed identification of 21,580 protein groups in the cell lines dataset (MQ search results available in ‘txt-celllines’ folder), and 13,441 protein groups in the tumours dataset (MQ search results available in ‘txt-tumours’ folder).
HostingRepositoryPRIDE
AnnounceDate2019-07-21
AnnouncementXMLSubmission_2019-07-21_11:18:00.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAndrew Jarnuczak
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive; LTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-04-11 02:23:35ID requested
12019-07-21 11:18:05announced
Publication List
Geiger T, Wehner A, Schaab C, Cox J, Mann M, Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics, 11(3):M111.014050(2012) [pubmed]
Coscia F, Watters KM, Curtis M, Eckert MA, Chiang CY, Tyanova S, Montag A, Lastra RR, Lengyel E, Mann M, Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status. Nat Commun, 7():12645(2016) [pubmed]
Frejno M, Zenezini Chiozzi R, Wilhelm M, Koch H, Zheng R, Klaeger S, Ruprecht B, Meng C, Kramer K, Jarzab A, Heinzlmeir S, Johnstone E, Domingo E, Kerr D, Jesinghaus M, Slotta-Huspenina J, Weichert W, Knapp S, Feller SM, Kuster B, Pharmacoproteomic characterisation of human colon and rectal cancer. Mol Syst Biol, 13(11):951(2017) [pubmed]
10.1101/665968;
Pozniak Y, Balint-Lahat N, Rudolph JD, Lindskog C, Katzir R, Avivi C, Pontén F, Ruppin E, Barshack I, Geiger T, System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis. Cell Syst, 2(3):172-84(2016) [pubmed]
Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes. Cell Syst, 4(6):587-599.e4(2017) [pubmed]
Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM, Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. Gastroenterology, 153(4):1082-1095(2017) [pubmed]
Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, Carr SA, Gillette MA, Klauser KR, Kuhn E, Mani DR, Mertins P, Ketchum KA, Paulovich AG, Whiteaker JR, Edwards NJ, McGarvey PB, Madhavan S, Wang P, Chan D, Pandey A, Shih IeM, Zhang H, Zhang Z, Zhu H, Whiteley GA, Skates SJ, White FM, Levine DA, Boja ES, Kinsinger CR, Hiltke T, Mesri M, Rivers RC, Rodriguez H, Shaw KM, Stein SE, Fenyo D, Liu T, McDermott JE, Payne SH, Rodland KD, Smith RD, Rudnick P, Snyder M, Zhao Y, Chen X, Ransohoff DF, Hoofnagle AN, Liebler DC, Sanders ME, Shi Z, Slebos RJ, Tabb DL, Zhang B, Zimmerman LJ, Wang Y, Davies SR, Ding L, Ellis MJ, Townsend RR, Proteogenomic characterization of human colon and rectal cancer. Nature, 513(7518):382-7(2014) [pubmed]
Lawrence RT, Perez EM, Hernández D, Miller CP, Haas KM, Irie HY, Lee SI, Blau CA, Villén J, The proteomic landscape of triple-negative breast cancer. Cell Rep, 11(4):630-44(2015) [pubmed]
Iglesias-Gato D, Wikström P, Tyanova S, Lavallee C, Thysell E, Carlsson J, Hägglöf C, Cox J, Andrén O, Stattin P, Egevad L, Widmark A, Bjartell A, Collins CC, Bergh A, Geiger T, Mann M, Flores-Morales A, The Proteome of Primary Prostate Cancer. Eur Urol, 69(5):942-52(2016) [pubmed]
Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, Proteomic maps of breast cancer subtypes. Nat Commun, 7():10259(2016) [pubmed]
Gholami AM, Hahne H, Wu Z, Auer FJ, Meng C, Wilhelm M, Kuster B, Global proteome analysis of the NCI-60 cell line panel. Cell Rep, 4(3):609-20(2013) [pubmed]
Keyword List
submitter keyword: cell lines, tumours, quantification, meta-analysis, public data reuse, reanalysis
Contact List
Juan Antonio Vizcaíno
contact affiliationEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
contact emailjuan@ebi.ac.uk
lab head
Andrew Jarnuczak
contact affiliationEBI
contact emailjarnuczak@ebi.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
PRIDE project URI
Repository Record List
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