PXD013455

PXD013455 is an original dataset announced via ProteomeXchange.

Dataset Summary

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).
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:33.511.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Jarnuczak
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive; LTQ Orbitrap

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-11 02:23:35	ID requested
1	2019-07-21 11:18:05	announced
⏵ 2	2023-11-14 08:50:48	announced	2023-11-14: Updated project metadata.

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]
Pozniak Y, Balint-Lahat N, Rudolph JD, Lindskog C, Katzir R, Avivi C, Pont, é, n 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, S, ø, rensen KD, H, ø, yer S, Ø, rntoft 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, Hern, á, ndez D, Miller CP, Haas KM, Irie HY, Lee SI, Blau CA, Vill, é, n J, The proteomic landscape of triple-negative breast cancer. Cell Rep, 11(4):630-44(2015) [pubmed]
Iglesias-Gato D, Wikstr, ö, m P, Tyanova S, Lavallee C, Thysell E, Carlsson J, H, ä, ggl, ö, f C, Cox J, Andr, é, n 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]

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]

Pozniak Y, Balint-Lahat N, Rudolph JD, Lindskog C, Katzir R, Avivi C, Pont, é, n 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, S, ø, rensen KD, H, ø, yer S, Ø, rntoft 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, Hern, á, ndez D, Miller CP, Haas KM, Irie HY, Lee SI, Blau CA, Vill, é, n J, The proteomic landscape of triple-negative breast cancer. Cell Rep, 11(4):630-44(2015) [pubmed]

Iglesias-Gato D, Wikstr, ö, m P, Tyanova S, Lavallee C, Thysell E, Carlsson J, H, ä, ggl, ö, f C, Cox J, Andr, é, n 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: tumours, meta-analysis,cell lines, reanalysis, public data reuse, quantification

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

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	andrew.at.astra@gmail.com
dataset submitter

Full Dataset Link List

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/2019/07/PXD013455
PRIDE project URI

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/2019/07/PXD013455

PRIDE project URI

Repository Record List

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