PXD014834

PXD014834 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue / Global Proteome Analysis of Normal Colon Epithelium Samples
Description	Explore This Study at the NCI Proteomic Data Commons The goal of the CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue is to analyze the proteomes of TCGA tumor samples that have been comprehensively characterized by molecular methods (Cancer Genome Atlas Network, Nature 2012). Ninety-five TCGA tumor samples were used in this study from 90 patients, with 5 samples representing different portions from the same tumor. The samples originated from two TCGA cohorts: 64 are from Colon Adenocarcinoma (COAD) samples and 31 are from the Rectum Adenocarcinoma (READ) collection. The primary data from the liquid chromatography-tandem mass spectrometry (LC-MS/MS) global proteomic profiling of each tumor sample is associated with a data set in the table below. This work was accomplished by the Proteome Characterization Center (PCC) at Vanderbilt University led by Dr. Daniel C. Liebler. Clinical data files contain both the human readable TCGA bar codes and the UUIDs for each sample. Complete Data Analysis from Vanderbilt University as published in Nature (Zhang, B., et al., Nature (2014) doi:10.1038/nature13438 Published online) is available here. Data available on this study page (peptide spectrum matches and protein reports) are from the CPTAC Common Data Analysis Pipeline. COAD tumor sample genomic data can be downloaded from here. READ tumor sample genomic data can be downloaded from here. Colon tissue samples (ascending and descending) were obtained from 30 patients. Each sample was analyzed with label free global proteomic profiling. These colon samples, while derived from colon cancer subjects, did not contain tumor. Samples were obtained from the Jim Ayers Institute for Precancer Detection and Diagnosis. Data sets below are labeled with the patient identification number and contain data for both ascending and descending tissue samples. Data from colon tumor samples are available in the TCGA Colorectal Cancer study. Dataset imported into MassIVE from https://cptac-data-portal.georgetown.edu/cptac/s/S016 and https://cptac-data-portal.georgetown.edu/cptac/s/S019 on 06/23/16 Dataset source: https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome
HostingRepository	MassIVE
AnnounceDate	2020-03-31
AnnouncementXML	Submission_2024-03-15_16:35:36.268.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christopher Kinsinger
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl; Acetyl; Deamidated; Glu->pyro-Glu; Gln->pyro-Glu
Instrument	LTQ Orbitrap Velos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-30 20:24:49	ID requested
⏵ 1	2024-03-15 16:35:37	announced

Publication List

Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, Kovar CL, Lewis LR, Morgan MB, Newsham IF, Reid JG, Santibanez J, Shinbrot E, Trevino LR, Wu YQ, Wang M, Gunaratne P, Donehower LA, Creighton CJ, Wheeler DA, Gibbs RA, Lawrence MS, Voet D, Jing R, Cibulskis K, Sivachenko A, Stojanov P, McKenna A, Lander ES, Gabriel S, Getz G, Ding L, Fulton RS, Koboldt DC, Wylie T, Walker J, Dooling DJ, Fulton L, Delehaunty KD, Fronick CC, Demeter R, Mardis ER, Wilson RK, Chu A, Chun HJ, Mungall AJ, Pleasance E, Robertson A, Stoll D, Balasundaram M, Birol I, Butterfield YS, Chuah E, Coope RJ, Dhalla N, Guin R, Hirst C, Hirst M, Holt RA, Lee D, Li HI, Mayo M, Moore RA, Schein JE, Slobodan JR, Tam A, Thiessen N, Varhol R, Zeng T, Zhao Y, Jones SJ, Marra MA, Bass AJ, Ramos AH, Saksena G, Cherniack AD, Schumacher SE, Tabak B, Carter SL, Pho NH, Nguyen H, Onofrio RC, Crenshaw A, Ardlie K, Beroukhim R, Winckler W, Getz G, Meyerson M, Protopopov A, Zhang J, Hadjipanayis A, Lee E, Xi R, Yang L, Ren X, Zhang H, Sathiamoorthy N, Shukla S, Chen PC, Haseley P, Xiao Y, Lee S, Seidman J, Chin L, Park PJ, Kucherlapati R, Auman JT, Hoadley KA, Du Y, Wilkerson MD, Shi Y, Liquori C, Meng S, Li L, Turman YJ, Topal MD, Tan D, Waring S, Buda E, Walsh J, Jones CD, Mieczkowski PA, Singh D, Wu J, Gulabani A, Dolina P, Bodenheimer T, Hoyle AP, Simons JV, Soloway M, Mose LE, Jefferys SR, Balu S, O'Connor BD, Prins JF, Chiang DY, Hayes D, Perou CM, Hinoue T, Weisenberger DJ, Maglinte DT, Pan F, Berman BP, Van Den Berg DJ, Shen H, Triche T, Baylin SB, Laird PW, Getz G, Noble M, Voet D, Saksena G, Gehlenborg N, DiCara D, Zhang J, Zhang H, Wu CJ, Liu SY, Shukla S, Lawrence MS, Zhou L, Sivachenko A, Lin P, Stojanov P, Jing R, Park RW, Nazaire MD, Robinson J, Thorvaldsdottir H, Mesirov J, Park PJ, Chin L, Thorsson V, Reynolds SM, Bernard B, Kreisberg R, Lin J, Iype L, Bressler R, Erkkil, ä T, Gundapuneni M, Liu Y, Norberg A, Robinson T, Yang D, Zhang W, Shmulevich I, de Ronde JJ, Schultz N, Cerami E, Ciriello G, Goldberg AP, Gross B, Jacobsen A, Gao J, Kaczkowski B, Sinha R, Aksoy B, Antipin Y, Reva B, Shen R, Taylor BS, Chan TA, Ladanyi M, Sander C, Akbani R, Zhang N, Broom BM, Casasent T, Unruh A, Wakefield C, Hamilton SR, Cason R, Baggerly KA, Weinstein JN, Haussler D, Benz CC, Stuart JM, Benz SC, Sanborn J, Vaske CJ, Zhu J, Szeto C, Scott GK, Yau C, Ng S, Goldstein T, Ellrott K, Collisson E, Cozen AE, Zerbino D, Wilks C, Craft B, Spellman P, Penny R, Shelton T, Hatfield M, Morris S, Yena P, Shelton C, Sherman M, Paulauskis J, Gastier-Foster JM, Bowen J, Ramirez NC, Black A, Pyatt R, Wise L, White P, Bertagnolli M, Brown J, Chan TA, Chu GC, Czerwinski C, Denstman F, Dhir R, D, ö, rner A, Fuchs CS, Guillem JG, Iacocca M, Juhl H, Kaufman A, Kohl B, Van Le X, Mariano MC, Medina EN, Meyers M, Nash GM, Paty PB, Petrelli N, Rabeno B, Richards WG, Solit D, Swanson P, Temple L, Tepper JE, Thorp R, Vakiani E, Weiser MR, Willis JE, Witkin G, Zeng Z, Zinner MJ, Zornig C, Jensen MA, Sfeir R, Kahn AB, Chu AL, Kothiyal P, Wang Z, Snyder EE, Pontius J, Pihl TD, Ayala B, Backus M, Walton J, Whitmore J, Baboud J, Berton DL, Nicholls MC, Srinivasan D, Raman R, Girshik S, Kigonya PA, Alonso S, Sanbhadti RN, Barletta SP, Greene JM, Pot DA, Shaw KR, Dillon LA, Buetow K, Davidsen T, Demchok JA, Eley G, Ferguson M, Fielding P, Schaefer C, Sheth M, Yang L, Guyer MS, Ozenberger BA, Palchik JD, Peterson J, Sofia HJ, Thomson E, Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487(7407):330-7(2012) [pubmed]

Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, Kovar CL, Lewis LR, Morgan MB, Newsham IF, Reid JG, Santibanez J, Shinbrot E, Trevino LR, Wu YQ, Wang M, Gunaratne P, Donehower LA, Creighton CJ, Wheeler DA, Gibbs RA, Lawrence MS, Voet D, Jing R, Cibulskis K, Sivachenko A, Stojanov P, McKenna A, Lander ES, Gabriel S, Getz G, Ding L, Fulton RS, Koboldt DC, Wylie T, Walker J, Dooling DJ, Fulton L, Delehaunty KD, Fronick CC, Demeter R, Mardis ER, Wilson RK, Chu A, Chun HJ, Mungall AJ, Pleasance E, Robertson A, Stoll D, Balasundaram M, Birol I, Butterfield YS, Chuah E, Coope RJ, Dhalla N, Guin R, Hirst C, Hirst M, Holt RA, Lee D, Li HI, Mayo M, Moore RA, Schein JE, Slobodan JR, Tam A, Thiessen N, Varhol R, Zeng T, Zhao Y, Jones SJ, Marra MA, Bass AJ, Ramos AH, Saksena G, Cherniack AD, Schumacher SE, Tabak B, Carter SL, Pho NH, Nguyen H, Onofrio RC, Crenshaw A, Ardlie K, Beroukhim R, Winckler W, Getz G, Meyerson M, Protopopov A, Zhang J, Hadjipanayis A, Lee E, Xi R, Yang L, Ren X, Zhang H, Sathiamoorthy N, Shukla S, Chen PC, Haseley P, Xiao Y, Lee S, Seidman J, Chin L, Park PJ, Kucherlapati R, Auman JT, Hoadley KA, Du Y, Wilkerson MD, Shi Y, Liquori C, Meng S, Li L, Turman YJ, Topal MD, Tan D, Waring S, Buda E, Walsh J, Jones CD, Mieczkowski PA, Singh D, Wu J, Gulabani A, Dolina P, Bodenheimer T, Hoyle AP, Simons JV, Soloway M, Mose LE, Jefferys SR, Balu S, O'Connor BD, Prins JF, Chiang DY, Hayes D, Perou CM, Hinoue T, Weisenberger DJ, Maglinte DT, Pan F, Berman BP, Van Den Berg DJ, Shen H, Triche T, Baylin SB, Laird PW, Getz G, Noble M, Voet D, Saksena G, Gehlenborg N, DiCara D, Zhang J, Zhang H, Wu CJ, Liu SY, Shukla S, Lawrence MS, Zhou L, Sivachenko A, Lin P, Stojanov P, Jing R, Park RW, Nazaire MD, Robinson J, Thorvaldsdottir H, Mesirov J, Park PJ, Chin L, Thorsson V, Reynolds SM, Bernard B, Kreisberg R, Lin J, Iype L, Bressler R, Erkkil, ä T, Gundapuneni M, Liu Y, Norberg A, Robinson T, Yang D, Zhang W, Shmulevich I, de Ronde JJ, Schultz N, Cerami E, Ciriello G, Goldberg AP, Gross B, Jacobsen A, Gao J, Kaczkowski B, Sinha R, Aksoy B, Antipin Y, Reva B, Shen R, Taylor BS, Chan TA, Ladanyi M, Sander C, Akbani R, Zhang N, Broom BM, Casasent T, Unruh A, Wakefield C, Hamilton SR, Cason R, Baggerly KA, Weinstein JN, Haussler D, Benz CC, Stuart JM, Benz SC, Sanborn J, Vaske CJ, Zhu J, Szeto C, Scott GK, Yau C, Ng S, Goldstein T, Ellrott K, Collisson E, Cozen AE, Zerbino D, Wilks C, Craft B, Spellman P, Penny R, Shelton T, Hatfield M, Morris S, Yena P, Shelton C, Sherman M, Paulauskis J, Gastier-Foster JM, Bowen J, Ramirez NC, Black A, Pyatt R, Wise L, White P, Bertagnolli M, Brown J, Chan TA, Chu GC, Czerwinski C, Denstman F, Dhir R, D, ö, rner A, Fuchs CS, Guillem JG, Iacocca M, Juhl H, Kaufman A, Kohl B, Van Le X, Mariano MC, Medina EN, Meyers M, Nash GM, Paty PB, Petrelli N, Rabeno B, Richards WG, Solit D, Swanson P, Temple L, Tepper JE, Thorp R, Vakiani E, Weiser MR, Willis JE, Witkin G, Zeng Z, Zinner MJ, Zornig C, Jensen MA, Sfeir R, Kahn AB, Chu AL, Kothiyal P, Wang Z, Snyder EE, Pontius J, Pihl TD, Ayala B, Backus M, Walton J, Whitmore J, Baboud J, Berton DL, Nicholls MC, Srinivasan D, Raman R, Girshik S, Kigonya PA, Alonso S, Sanbhadti RN, Barletta SP, Greene JM, Pot DA, Shaw KR, Dillon LA, Buetow K, Davidsen T, Demchok JA, Eley G, Ferguson M, Fielding P, Schaefer C, Sheth M, Yang L, Guyer MS, Ozenberger BA, Palchik JD, Peterson J, Sofia HJ, Thomson E, Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487(7407):330-7(2012) [pubmed]

Keyword List

submitter keyword: CPTAC

submitter keyword: CPTAC

Contact List

Dr. Daniel C. Liebler and Jim Ayers
lab head
Christopher Kinsinger
contact affiliation	NIH/NCI
contact email	Christopher.kinsinger@nih.gov
dataset submitter

Full Dataset Link List

MassIVE dataset 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://massive.ucsd.edu/MSV000079852/

MassIVE dataset 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://massive.ucsd.edu/MSV000079852/