PXD013455

DataSet Summary

• HostingRepository: PRIDE
• AnnounceDate: 2019-07-21
• AnnouncementXML: Submission_2019-07-21_11:18:00.xml
• DigitalObjectIdentifier:
• ReviewLevel: Peer-reviewed dataset
• DatasetOrigin: Original data
• RepositorySupport: Unsupported dataset by repository
• PrimarySubmitter: Andrew Jarnuczak
• Title: The landscape of protein expression in cancer based on public proteomics data
• Description: This 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).
• SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
• ModificationList: acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
• Instrument: Q Exactive; LTQ Orbitrap

Dataset History

Version	Datetime	Status	ChangeLog Entry
0	2019-04-11 02:23:35	ID requested
1	2019-07-21 11:18:05	announced

Publication List

1. 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]
2. 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]
3. 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]
4. 10.1101/665968;
5. 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]
6. 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]
7. 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]
8. 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]
9. 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]
10. 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]
11. Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, Proteomic maps of breast cancer subtypes. Nat Commun, 7():10259(2016) [pubmed]
12. 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

1. submitter keyword: cell lines, tumours, quantification, meta-analysis, public data reuse, reanalysis

Contact List

Juan Antonio Vizcaíno
• contact affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
• contact email: juan@ebi.ac.uk
• lab head:
Andrew Jarnuczak
• contact affiliation: EBI
• contact email: jarnuczak@ebi.ac.uk
• dataset submitter:

Full Dataset Link List

1. Dataset FTP location
2. PRIDE project URI

Repository Record List

• PRIDE
  1. PXD013455
     1. Label: PRIDE project
     2. Name: The landscape of protein expression in cancer based on public proteomics data