{"_id":"5949471bcb42790024c9d3f8","project":"55faf11ba62ba1170021a9a7","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":38,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"58458b4fba4f1c0f009692bb","project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"user":"5613e4f8fdd08f2b00437620","__v":0,"parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-06-20T16:02:35.023Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"settings":"","results":{"codes":[]},"auth":"required","params":[],"url":""},"isReference":false,"order":8,"body":"##Overview\n\nThe [Clinical Proteomic Tumor Analysis Consortium (CPTAC)](https://proteomics.cancer.gov/programs/cptac) is a comprehensive and coordinated effort to accelerate understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows.\n\nThe CPTAC analyzes cancer biospecimens from genomics initiatives such as [The Cancer Genome Atlas (TCGA)](https://cancergenome.nih.gov/) by mass spectrometry to characterize and quantify their constituent proteins or “proteome”. These mass spectrometry data are present in four different file formats: raw, mzML, psm, and mzid. Raw files contain raw mass spectrometry spectra in vendor-specific file formats corresponding to the mass spectrometers used to acquire the spectra. The [mzML](http://www.psidev.info/mzml) files are generated by converting these raw files to a [HUPO Proteome Standards Initiative (PSI)](http://www.psidev.info/)-compliant format. The psm files report the peptide spectrum match (PSM) data obtained by processing the mzML files. The mzID files were generated by converting the psm files to the HUPO PSI-compliant mzldentML format.\n\nLearn more about the [metadata](doc:cptac-metadata) associated with CPTAC data on the CGC.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Distribution of the data\n\nMass spectrometry enables the highly specific identification of proteins and proteoforms, accurate relative quantitation of protein abundance in contrasting biospecimens, and the localization of post-translational protein modifications (such as phosphorylation) on a protein’s sequence. Mass spectrometry (MS) data from four [TCGA cancer types](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations) (TCGA-OV, TCGA-BRCA, TCGA-COAD, TCGA-READ) are included in the CPTAC public project.\n\nSee below for an overview of the number of samples, type of analytics, and experiment strategies available for each cancer type.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Collection\",\n    \"h-1\": \"Samples\",\n    \"h-2\": \"Analytics\",\n    \"h-3\": \"Experiments\",\n    \"0-0\": \"TCGA-OV\",\n    \"0-1\": \"174\",\n    \"0-2\": \"Proteome, Phosphoproteome\",\n    \"0-3\": \"4-plex iTRAQ MS\",\n    \"1-0\": \"TCGA-BRCA\",\n    \"1-1\": \"105\",\n    \"1-2\": \"Proteome, Phosphoproteome\",\n    \"1-3\": \"4-plex iTRAQ MS\",\n    \"2-0\": \"TCGA-COAD\",\n    \"2-1\": \"64\",\n    \"2-2\": \"Proteome\",\n    \"2-3\": \"MS\",\n    \"3-0\": \"TCGA-READ\",\n    \"3-1\": \"31\",\n    \"3-2\": \"Proteome\",\n    \"3-3\": \"MS\"\n  },\n  \"cols\": 4,\n  \"rows\": 4\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##ACCESS CPTAC DATA\n\nAccess a repository of CPTAC files via the [Data Browser](doc:about-the-data-browser) or via the [CPTAC dataset Project](doc:the-clinical-proteomic-tumor-analysis-consortium-cptac-project).\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"","slug":"cptac-data","type":"basic","title":"CPTAC data"}
##Overview The [Clinical Proteomic Tumor Analysis Consortium (CPTAC)](https://proteomics.cancer.gov/programs/cptac) is a comprehensive and coordinated effort to accelerate understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows. The CPTAC analyzes cancer biospecimens from genomics initiatives such as [The Cancer Genome Atlas (TCGA)](https://cancergenome.nih.gov/) by mass spectrometry to characterize and quantify their constituent proteins or “proteome”. These mass spectrometry data are present in four different file formats: raw, mzML, psm, and mzid. Raw files contain raw mass spectrometry spectra in vendor-specific file formats corresponding to the mass spectrometers used to acquire the spectra. The [mzML](http://www.psidev.info/mzml) files are generated by converting these raw files to a [HUPO Proteome Standards Initiative (PSI)](http://www.psidev.info/)-compliant format. The psm files report the peptide spectrum match (PSM) data obtained by processing the mzML files. The mzID files were generated by converting the psm files to the HUPO PSI-compliant mzldentML format. Learn more about the [metadata](doc:cptac-metadata) associated with CPTAC data on the CGC. <div align="right"><a href="#top">top</a></div> ##Distribution of the data Mass spectrometry enables the highly specific identification of proteins and proteoforms, accurate relative quantitation of protein abundance in contrasting biospecimens, and the localization of post-translational protein modifications (such as phosphorylation) on a protein’s sequence. Mass spectrometry (MS) data from four [TCGA cancer types](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations) (TCGA-OV, TCGA-BRCA, TCGA-COAD, TCGA-READ) are included in the CPTAC public project. See below for an overview of the number of samples, type of analytics, and experiment strategies available for each cancer type. [block:parameters] { "data": { "h-0": "Collection", "h-1": "Samples", "h-2": "Analytics", "h-3": "Experiments", "0-0": "TCGA-OV", "0-1": "174", "0-2": "Proteome, Phosphoproteome", "0-3": "4-plex iTRAQ MS", "1-0": "TCGA-BRCA", "1-1": "105", "1-2": "Proteome, Phosphoproteome", "1-3": "4-plex iTRAQ MS", "2-0": "TCGA-COAD", "2-1": "64", "2-2": "Proteome", "2-3": "MS", "3-0": "TCGA-READ", "3-1": "31", "3-2": "Proteome", "3-3": "MS" }, "cols": 4, "rows": 4 } [/block] <div align="right"><a href="#top">top</a></div> ##ACCESS CPTAC DATA Access a repository of CPTAC files via the [Data Browser](doc:about-the-data-browser) or via the [CPTAC dataset Project](doc:the-clinical-proteomic-tumor-analysis-consortium-cptac-project). <div align="right"><a href="#top">top</a></div>