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For the full experience enable JavaScript in your browser.</div></noscript> </div> </div> <div class="row content-row"> <div class="content-left"> <div name="webpart" id="webpart_8" ><div class="panel panel-portal"> <div class="panel-heading"><h3 class="panel-title pull-left" title="Panorama: A Repository for Targeted Mass Spectrometry Assays from Skyline"><a id="Panorama:ARepositoryforTargetedMassSpectrometryAssaysfromSkyline" class="labkey-anchor-disabled"><a href="/home/wiki-page.view?name=default"><span class="labkey-wp-title-text">Panorama: A Repository for Targeted Mass Spectrometry Assays from Skyline</span></a></a></h3> <span class="dropdown dropdown-rollup pull-right"><a href="#" data-toggle="dropdown" class="dropdown-toggle fa fa-caret-down"></a><ul class="dropdown-menu dropdown-menu-right"><li><a id='popupMenuView00012' href="/home/wiki-page.view?name=default&_print=1" tabindex="0" style="" rel="nofollow">Print</a></li></ul></span><div class="clearfix"></div></div> <div id="WebPartView1664915875" class=" panel-body">  <div class="labkey-wiki"><style xmlns="http://www.w3.org/1999/xhtml"> td.announcement { background-color: #134277; 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There is HTML markup in some of the descriptions. txt.innerHTML += html; textsContainer.appendChild(txt); } function appendToSlideshow(json) { addSlides(json); // Remove the blank placeholders const placeholderSlide = document.getElementById("blank_coverslide"); if (placeholderSlide) placeholderSlide.remove(); const placeholderText = document.getElementById("blank_coverslide_text"); if (placeholderText) placeholderText.remove(); // showSlides(); appendHardCodedSlides(); showSlides(); } </script> </tbody> </table> </td>  <td align="center" style="padding-right: 50px;" valign="top"> </td> </tr> </tbody> </table> </div> <br> <table width="100%"> <tbody><tr> <td align="center" colspan="2"> <a class="banner-button" href="/project/Panorama%20Public/begin.view" style="text-align:center">Panorama Public</a> <span>Browse the Panorama Public repository</span> </td> </tr> <tr> <td width="80%"> <p class="banner">Panorama is a server-based data repository application for targeted mass spectrometry assays that integrates into a <a href="https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view?">Skyline</a> mass spec workflow. It is implemented as a module within <a href="https://www.labkey.org/">LabKey Server</a>, an open-source bioinformatics data management platform with extensive support for proteomics and small molecule data, other assay data, and a security model rich enough to support clinical studies. Free projects are available on <a href="/home/support/wiki-page.view?name=hosted-project-signup-form">Sign Up</a>, and <a href="https://www.labkey.com/products-services/panorama-partners-program/">paid support is available for groups needing their own installation</a>.</p> </td> <td nowrap valign="top" width="20%"> <p class="banner-links"> [<a href="/labkey/wiki/home/page.view?name=Importing%20data%20into%20Panorama">Importing data into Panorama</a>]<br> [<a href="/labkey/wiki/home/page.view?name=tutorials">Tutorials</a>] <br> [<a href="/labkey/wiki/home/page.view?name=examples">Examples</a>]<br> [<a href="/labkey/issues/home/list.view?">Issues</a>]<br> [<a href="/labkey/project/home/support/begin.view">Support</a>]<br> [<a href="/labkey/wiki/home/support/page.view?name=hosted-project-signup-form">Sign Up</a>] </p> </td> </tr> </tbody></table> <h2>Get Started</h2> <div class="getstarted"> <table class="format"> <tbody> <tr> <td valign="top" width="36%"> <p><strong>Webinars</strong></p> <a href="/home/wiki-page.view?name=webinars"><img alt="Webinars" height="116" src="/home/wiki-download.view?entityId=ab4dea39-4e28-1030-8928-134f01698911&name=icon_webinars.png" width="165"></a> <ul> <li><span class="new">New! </span><a href="https://www.labkey.com/webinar/lc-ms-system-suitability-skyline-panorama/" target="_blank">System Suitability Best Practices with Skyline and Panorama hosted by LabKey</a></li> <li><a href="https://www.labkey.com/webinar/panorama-targeted-proteomics-research/" target="_blank">Introduction to Panorama 17.2 hosted by LabKey</a></li> <li><a href="https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/events/2015%20Webinars/Webinar%2011/begin.view?">Panorama Public and Panorama AutoQC</a></li> <li><a href="/home/wiki-page.view?name=webinar3">Panorama: Managing and Analyzing Large Datasets </a></li> <li><a href="/home/wiki-page.view?name=webinar2">Panorama Targeted Proteomics Knowledgebase</a></li> <li><a href="/home/wiki-page.view?name=webinar1">Panorama: An Introduction</a></li> </ul>  </td> <td valign="top" width="30%"> <p><strong>Tutorials</strong></p> <a class="labkey-text-link" href="/home/wiki-page.view?name=tutorials"><img alt="Tutorials" height="116" src="/home/wiki-download.view?entityId=ab4dea39-4e28-1030-8928-134f01698911&name=icon_tutorials.png" width="146"></a> <ul> <li><a href="/home/wiki-page.view?name=sharing_documents">Sharing Skyline Documents</a></li> <li><a href="/home/wiki-page.view?name=chromatogram_libraries">Panorama Chromatogram Libraries</a></li> <li><a href="/home/wiki-page.view?name=panorama_public">Publish to Panorama Public</a></li> </ul>  </td> </tr> </tbody> </table> </div> <table class="format" width="100%"> <tbody><tr> <td> <p><br>Panorama was developed with the following goals for targeted proteomics investigation:</p> <ul> <li>Help labs aggregate curated results</li> <li>Store the complete Skyline document data model</li> <li>Use previous experiments to inform new experiments</li> <li>Make it easy to search and review a large body of experiments</li> <li>Facilitate sharing results</li> <li>Keep private data secure</li> </ul> <p>Panorama was designed to integrate with existing Skyline workflows.  Users can publish their documents to a Panorama server directly from Skyline.  Data on the server can be organized in folders, and users can take advantage of LabKey Server's fine-grained permission controls to securely share data with collaborators, or make it publicly available.  You can browse through some of the <a href="#examples">example experiments</a> below to explore the Panorama UI for published Skyline documents. </p> <p><strong>PanoramaWeb</strong> is a public Panorama server hosted at the University of Washington where laboratories and organizations can own free projects.  You can request a project on this server to find out what Panorama has to offer, without having to set up and maintain your own LabKey Server.  You will be able to explore all the available features in Panorama, and be given administrative rights to your project so that you can set up folders and configure permissions.  The LabKey Server security infrastructure will allow you to keep your data as private as you want or release it publicly when you are ready.</p> <p>Panorama can also be installed by laboratories and organizations on their own servers.  Look at <a href="/labkey/wiki/home/page.view?name=Install%20Panorama">Install Panorama</a> to get started. </p> </td> </tr> </tbody></table> <h2>Events</h2> <table class="format" width="100%"> <tbody><tr> <td valign="middle" width="60%"> <p><strong>Skyline User Group Meeting Online before ASMS 2020</strong> <br>  <a href="https://skyline.ms/project/home/software/Skyline/events/2020%20User%20Group%20Meeting%20at%20ASMS/begin.view?" target="_blank">Review the presentations</a> </p> <p><strong>Skyline User Group Meeting at ASMS 2019</strong> <br>  <a href="https://skyline.ms/project/home/software/Skyline/events/2019%20User%20Group%20Meeting%20at%20ASMS/begin.view?" target="_blank">Review the presentations</a> </p> <p><strong>Skyline User Group Meeting at ASMS 2018</strong> <br>  <a href="https://skyline.ms/project/home/software/Skyline/events/2018%20User%20Group%20Meeting%20at%20ASMS/begin.view?" target="_blank">Review the presentations</a> </p> <p><strong>Skyline User Group Meeting at ASMS 2017</strong> <br>  <a href="https://skyline.ms/project/home/software/Skyline/events/2017%20User%20Group%20Meeting%20at%20ASMS/begin.view?" target="_blank">Review the presentations</a> </p> <p><strong>Skyline User Group Meeting at ASMS 2016</strong> <br>  <a href="https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/events/2016%20User%20Group%20Meeting%20at%20ASMS/begin.view?" target="_blank">Review the presentations</a> </p>  </td>  </tr> </tbody></table>  <h2>Recently Published</h2> <table class="format"> <tbody> <tr> <td> <p> Panorama Public: A public repository for quantitative data sets processed in Skyline <em> Vagisha Sharma, Josh Eckels, Birgit Schilling, Christina Ludwig, Jacob D. Jaffe, Michael J. MacCoss and Brendan MacLean. </em> Molecular and Cellular Proteomics. 2018 <br> [<a href="https://doi.org/10.1074/MCP.RA117.000543" target="_blank">abstract</a>] [<a href="https://www.mcponline.org/content/mcprot/17/6/1239.full.pdf" target="_blank">pdf</a>] </p></td> </tr> <tr> <td> <p>An Automated Pipeline to Monitor System Performance in Liquid Chromatography Tandem Mass Spectrometry Proteomic Experiments <em>Michael S. Bereman, Joshua Beri, Vagisha Sharma, Cory Nathe, Josh Eckels, Brendan MacLean, Michael J. MacCoss<em>. Journal of Proteome Research</em></em>. 2016 <br> [<a href="http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00744" target="_blank">abstract</a>] [<a href="http://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.6b00744" target="_blank">pdf</a>] </p></td> </tr> <tr> <td> <p>Panorama Public: ProteomeXchange and Cloud Storage Integration. <em>Sharma V, Connolly B, Eckels J, Bradlee D, Omaiye A, MacCoss MJ, MacLean B<i>. ASMS Poster</i></em>. 2019 <br> [<a href="/_webdav/home/%40files/ASMS_2019_PanoramaPublic.pdf?renderAs=DEFAULT" target="_blank">pdf</a>]</p> </td> </tr> <tr> <td> <p>Customizable quality control metrics and notifications with Panorama, AutoQC, and Skyline. <em>Eckels J, Sharma V, Pradere M, Juneja A, Omaiye A, Nathe C, Jewargikar S, MacCoss MJ, MacLean B<i>. ASMS Poster</i></em>. 2019 <br> [<a href="/_webdav/home/%40files/2019-ASMS-Panorama-QC-update.pdf?renderAs=DEFAULT" target="_blank">pdf</a>]</p> </td> </tr> <tr> <td> <p>Audit Logs to enforce document integrity in Skyline and Panorama. <em>Rhode T, Chupalov R, Shulman N, Sharma V, Eckels J, Pratt BS, MacCoss MJ, MacLean B<i>. ASMS Poster</i></em>. 2019 <br> [<a href="/_webdav/home/%40files/ASMS-2019-Audit-Logging.pdf?renderAs=DEFAULT" target="_blank">pdf</a>]</p> </td> </tr> <tr> <td> <p>Managing Small Molecule Targeted Mass Spec Assays using Skyline and Panorama. <em>Eckels J, Sharma V, Pratt B, Dunkley T, Wildsmith K, Anania V, Li Q, Nathe C, Patel B, MacCoss MJ, MacLean B<i>. ASMS Poster</i></em>. 2016 <br> [<a href="/labkey/_webdav/home/%40files/2016-ASMS-Panorama-small-molecule-poster-v5.pdf?renderAs=DEFAULT" target="_blank">pdf</a>]</p> </td> </tr> <tr><td><a class="labkey-text-link" href="/home/wiki-page.view?name=publications">More Publications</a></td> </tr> </tbody> </table> <div class="labkey-page-nav"> <table width="100%"> <tbody><tr> <td align="left" class="homegrant" valign="middle" width="50%"><a href="https://skyline.ms/seattle-quant.url" target="_blank">Seattle Quant: A Resource for the Skyline Software Ecosystem</a></td> <td><a href="https://www.nigms.nih.gov/" target="_blank"><img src="https://compcellbio.org/assets/NIGMSLogoBGV2.png"></a></td> <td align="right" class="homegrant" valign="middle" width="50%">Funding provided by: <a href="https://www.nigms.nih.gov/Research/mechanisms/Pages/NIGMS-National-and-Regional-Resources-(R24).aspx" target="_blank">NIGMS National and Regional Resources (R24) Program</a></td> </tr> </tbody></table> </div> </div> <p/> </div></div></div> </div> <div class="content-right"> <div class="content-right-spacer"></div> <div name="webpart" id="webpart_10" ><div class="panel panel-portal"> <div class="panel-heading"><h3 class="panel-title pull-left" title="Pages"><a id="Pages" class="labkey-anchor-disabled"><span class="labkey-wp-title-text">Pages</span></a></h3><div class="clearfix"></div></div> <div id="WebPartView1916649469" class=" panel-body"><div id="NavTree-Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658"> <table class="labkey-nav-tree"><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree00013" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=default">Panorama: A Repository for Targeted Mass Spectrometry Assays from Skyline</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div 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href="/home/wiki-page.view?name=Create%20a%20folder%20in%20Panorama">Create a Folder in Panorama</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000111" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=folder_navigation">Folder Navigation in Panorama</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000112" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=add_project_users">Adding Users to a Project</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000113" class="labkey-nav-tree-text"> <a 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<td></td><td> <table class="labkey-nav-tree-child"><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000117" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=publish_to_panorama_public">Submit Data to Panorama Public</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000118" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=upload_raw_data">Upload Raw Data</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000119" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=upload_suppl_files">Upload Supplementary Files</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000120" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=include_subfolders">Include Subfolders in a Panorama Public Submission</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000121" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=px_data_validation">Data Validation for ProteomeXchange</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000122" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=unimod_matching">Finding Unimod Matches</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000123" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=download_public_data">Download Data From Panorama Public</a></td></tr></table> </td></tr> <tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <a id="navtree000124" href="/home/project-expandCollapse.view?path=%2FDocumentation%2FQuality%20control%20with%20AutoQC&treeId=Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658"><img src="/_images/plus.gif" width=9 height=9></a></td><td id="navtree000125" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=qc_with_panorama">Quality control with AutoQC</a></td></tr><tr style=display:none> <td></td><td> <table class="labkey-nav-tree-child"><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000126" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=autoqc_setup_tutorial">Lindsay Pino's AutoQC Setup Tutorial</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000127" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=upgrade-to-autoqc-24.1.0.x">Upgrading to AutoQC Loader 24.1.0.x</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <a id="navtree000128" href="/home/project-expandCollapse.view?path=%2FDocumentation%2FQuality%20control%20with%20AutoQC%2FAutoQC%20Loader%20Documentation&treeId=Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658"><img src="/_images/plus.gif" width=9 height=9></a></td><td id="navtree000129" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=autoqc_loader_doc">AutoQC Loader Documentation</a></td></tr><tr style=display:none> <td></td><td> <table class="labkey-nav-tree-child"><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000130" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=autoqc_1_1_0_20237_doc">AutoQC Loader 1.1.0.20237 Documentation</a></td></tr></table> </td></tr> <tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div 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id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=tutorials">Tutorials</a></td></tr><tr style=display:none> <td></td><td> <table class="labkey-nav-tree-child"><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000135" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=sharing_documents">Tutorial: Sharing Skyline Documents</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000136" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=chromatogram_libraries">Tutorial: Panorama Chromatogram Libraries</a></td></tr><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000137" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=panorama_public">Tutorial: Submitting Supplementary Data to Panorama Public</a></td></tr></table> </td></tr> <tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <a id="navtree000138" href="/home/project-expandCollapse.view?path=%2FWebinars&treeId=Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658"><img src="/_images/plus.gif" width=9 height=9></a></td><td id="navtree000139" class="labkey-nav-tree-text"> <a id="Wiki-TOC-4d45d992-4dee-1030-94b4-0dddb6ce1658" href="/home/wiki-page.view?name=webinars">Webinars</a></td></tr><tr style=display:none> <td></td><td> <table class="labkey-nav-tree-child"><tr class="labkey-nav-tree-row labkey-header"><td class="labkey-nav-tree-node"> <div class="labkey-nav-tree-indenter"></div></td><td id="navtree000140" class="labkey-nav-tree-text"> <a 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