{"_id":"5939ea7c16f8ad000f18d4a3","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":"5771811e27a5c20e00030dcd","version":"55faf11ba62ba1170021a9aa","__v":0,"project":"55faf11ba62ba1170021a9a7","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-27T19:40:14.237Z","from_sync":false,"order":7,"slug":"public-projects","title":"PUBLIC PROJECTS"},"user":"5613e4f8fdd08f2b00437620","__v":0,"parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-06-09T00:23:24.716Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":5,"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 CPTAC data data available on the CGC via [this public project](https://cgc.sbgenomics.com/u/sevenbridges/clinical-proteomic-tumor-analysis-consortium-cptac/).\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Access the CPTAC public project\n\nTo access the CPTAC public project:\n\n1. Click on **Public projects** from the top navigation bar.\n2. Select **Clinical Proteomic Tumor Analysis Consortium (CPTAC)**.\n\nYou'll be taken to the main dashboard of the CPTAC public project.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Use the CPTAC public project\nAll CGC users automatically have copy permissions for this project. This means that while you cannot upload data or tools to the public project, you can copy the available data to your own projects on the CGC to execute analyses.\n\nYou have the options to:\n  * **Copy the entire project -** Start from the copied project and add apps to execute analyses on CPTAC data.\n  * **Select and copy a subset of the data to your own project -** Use the selected data within your own analyses in your project.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Copy the entire project\n\n1. Access the CPTAC public project by selecting **Clinical Proteomic Tumor Analysis Consortium (CPTAC)** from **Public projects** in the top navigation bar.\n2. Click **Copy this project*,* next to the project's title.\n3. In the pop-up window, optionally name your copy of the project and select a billing group.\n4. Once you've customized the details, click **Copy** to copy the entire project.\n\nYou'll be redirected to the dashboard of your cloned project. Add apps to conduct analyses on the data in your project.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Use a subset of the data\n\nInstead of cloning the entire project, you can choose to select and copy a subset of the data.\n\n1. Access the CPTAC public project by selecting **Clinical Proteomic Tumor Analysis Consortium (CPTAC)** from **Public projects** in the top navigation bar.\n2. Click the **Files** tab. This will take you to the **Files** page for the CPTAC public project.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/8ae55e9-Screen_Shot_2017-06-20_at_11.51.01_AM.png\",\n        \"Screen Shot 2017-06-20 at 11.51.01 AM.png\",\n        1387,\n        615,\n        \"#f9f9f9\"\n      ]\n    }\n  ]\n}\n[/block]\n3. Filter or search for the desired files.\n4. Choose specific files by checking the corresponding box by each file name.\n5. Select as many files as you desire and click **Copy to**.\n6. Select your target project from the drop-down menu.\n\nNow, you can start using the CPTAC files you've added to your personal project in your own analysis.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"","slug":"the-clinical-proteomic-tumor-analysis-consortium-cptac-project","type":"basic","title":"The Clinical Proteomic Tumor Analysis Consortium (CPTAC) project"}

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) project


##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 CPTAC data data available on the CGC via [this public project](https://cgc.sbgenomics.com/u/sevenbridges/clinical-proteomic-tumor-analysis-consortium-cptac/). <div align="right"><a href="#top">top</a></div> ##Access the CPTAC public project To access the CPTAC public project: 1. Click on **Public projects** from the top navigation bar. 2. Select **Clinical Proteomic Tumor Analysis Consortium (CPTAC)**. You'll be taken to the main dashboard of the CPTAC public project. <div align="right"><a href="#top">top</a></div> ##Use the CPTAC public project All CGC users automatically have copy permissions for this project. This means that while you cannot upload data or tools to the public project, you can copy the available data to your own projects on the CGC to execute analyses. You have the options to: * **Copy the entire project -** Start from the copied project and add apps to execute analyses on CPTAC data. * **Select and copy a subset of the data to your own project -** Use the selected data within your own analyses in your project. <div align="right"><a href="#top">top</a></div> ##Copy the entire project 1. Access the CPTAC public project by selecting **Clinical Proteomic Tumor Analysis Consortium (CPTAC)** from **Public projects** in the top navigation bar. 2. Click **Copy this project*,* next to the project's title. 3. In the pop-up window, optionally name your copy of the project and select a billing group. 4. Once you've customized the details, click **Copy** to copy the entire project. You'll be redirected to the dashboard of your cloned project. Add apps to conduct analyses on the data in your project. <div align="right"><a href="#top">top</a></div> ##Use a subset of the data Instead of cloning the entire project, you can choose to select and copy a subset of the data. 1. Access the CPTAC public project by selecting **Clinical Proteomic Tumor Analysis Consortium (CPTAC)** from **Public projects** in the top navigation bar. 2. Click the **Files** tab. This will take you to the **Files** page for the CPTAC public project. [block:image] { "images": [ { "image": [ "https://files.readme.io/8ae55e9-Screen_Shot_2017-06-20_at_11.51.01_AM.png", "Screen Shot 2017-06-20 at 11.51.01 AM.png", 1387, 615, "#f9f9f9" ] } ] } [/block] 3. Filter or search for the desired files. 4. Choose specific files by checking the corresponding box by each file name. 5. Select as many files as you desire and click **Copy to**. 6. Select your target project from the drop-down menu. Now, you can start using the CPTAC files you've added to your personal project in your own analysis. <div align="right"><a href="#top">top</a></div>