{"id":2769,"date":"2016-11-10T13:48:12","date_gmt":"2016-11-10T18:48:12","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/msr\/?page_id=2769"},"modified":"2018-02-20T15:31:25","modified_gmt":"2018-02-20T20:31:25","slug":"bupid-top-down","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/msr\/software\/bupid-top-down\/","title":{"rendered":"BUPID Top-Down"},"content":{"rendered":"<h2>BUPID Top-Down: Software Tools for Analysis of Top-Down MS\/MS Spectra<\/h2>\n<p><span><b><strong>BUPID <\/strong><\/b>(Boston University Protein Identifier) <b><strong>Top-Down <\/strong><\/b>is a web-based platform developed at the <b><strong>Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA)<\/strong><\/b>. The platform provides the means to analyze top-down MS\/MS spectra obtained with a number of fragmentation methods, including CID, ECD, and ETD. Several software tools are available and may be used in any combination.<\/span><\/p>\n<h3>Tools Available<\/h3>\n<ul>\n<li><span>Deconvolution<\/span><\/li>\n<\/ul>\n<ul>\n<li><span>Protein identification<\/span><\/li>\n<\/ul>\n<ul>\n<li><span>Fragment ion assignment<\/span><\/li>\n<\/ul>\n<ul>\n<li><span>Sequence variant analysis<\/span><\/li>\n<\/ul>\n<ul>\n<li><span>Mass shift analysis<\/span><\/li>\n<\/ul>\n<h3>Input Requirements<\/h3>\n<ul>\n<li><span>Deconvoluted peak list or, for raw data, mzML or mzXML files without compression<br \/>\n<\/span><\/li>\n<\/ul>\n<ul>\n<li><span>Additional information depending on selected tools<br \/>\n<\/span><\/li>\n<\/ul>\n<h3>Output<\/h3>\n<ul>\n<li><span>Raw results in YAML format<\/span><\/li>\n<\/ul>\n<ul>\n<li><span>Built-in visualization tools<\/span><\/li>\n<\/ul>\n<ul>\n<li><span>Convenient download for further analysis (manual; other software)<\/span><\/li>\n<\/ul>\n<h3>Disclaimer<\/h3>\n<p><span>BUPID Top-Down was developed at the <b><strong>Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA)<\/strong><\/b>. The software tools are freely available for external testing. We assume no responsibility for their use, and we make no guarantees, whether expressed or implied, about their performance or any other characteristics. We would appreciate acknowledgment of our organization if BUPID Top-Down is used.<\/span><\/p>\n<p>If you are interested in\u00a0BUPID Top Down, please contact Prof. Mark McComb.<\/p>\n<h3>Publications<\/h3>\n<ul>\n<li><span><b><strong><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24687996\">Top-down tandem mass spectrometry on RNase A and B using a Qh\/FT-ICR hybrid mass spectrometer<\/a><\/strong><\/b><br \/>\nSandrine Bourgoin-Voillard, Nancy Leymarie, and Catherine E. Costello, <b><strong><em>Proteomics<\/em> 2014<\/strong><\/b>, 14(10), 1174-1184.<br \/>\nPMID: 24687996<br \/>\nPMCID: PMC4095805<br \/>\n[PubMed &#8211; in process]<br \/>\n<\/span><\/li>\n<\/ul>\n<ul>\n<li><span><b><strong><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3098445\">Top-down analysis of small plasma proteins using an LTQ-Orbitrap. Potential for mass spectrometry-based clinical assays for transthyretin and hemoglobin<\/a><\/strong><\/b><br \/>\nRoger Theberge, Giuseppe Infusini, Weiwei Tong, Mark E. McComb, and Catherine E. Costello, <b><strong><em>International Journal of Mass Spectrometry<\/em> 2011<\/strong><\/b>, 300(2-3), 130-142.<br \/>\nPMID: 21607198<br \/>\nPMCID: PMC3098445<br \/>\nNIHMSID: NIHMS245609<br \/>\n<\/span><\/li>\n<\/ul>\n<h3>Conference Presentations<\/h3>\n<ul>\n<li><span><b><strong><a href=\"\/msr\/files\/2016\/11\/ASMS-2016-BUPID-Heckendorf.pdf\">Top-down MSMS Data Analysis: Software and Algorithms for Protein Identification and Fragment Ion Assignment<\/a><\/strong><\/b><br \/>\nChristian Heckendorf, Roger Theberge, Deborah R. Leon, Kshitij Khatri, Jean L. Spencer, Catherine E. Costello, and Mark E. McComb, <b><strong>ASMS 2016<\/strong><\/b>, San Antonio, TX.<\/span><\/li>\n<\/ul>\n<ul>\n<li><span><b><strong><a href=\"\/msr\/files\/2016\/11\/ASMS-2015-BUPID-Heckendorf.pdf\">High Quality Top-Down Proteomics Analysis Using R<\/a><\/strong><\/b><br \/>\nChristian Heckendorf, Roger Theberge, Jean L. Spencer, Catherine E. Costello, and Mark E. McComb, <b><strong>ASMS 2015<\/strong><\/b>, St. Louis, MO.<\/span><\/li>\n<\/ul>\n<ul>\n<li><span><b><strong><a href=\"\/msr\/files\/2016\/11\/ASMS-2014-BUPID-Heckendorf.pdf\">Automated protein identification and sequencing using top-down MS data<\/a><\/strong><\/b><br \/>\nChristian Heckendorf, Roger Theberge, Jean L. Spencer, Catherine E. Costello, and Mark E. McComb, <b><strong>ASMS 2014<\/strong><\/b>, Baltimore, MD.<\/span><\/li>\n<\/ul>\n<ul>\n<li><span><b><strong><a href=\"\/msr\/files\/2016\/11\/ASMS-2013-BUPID-Heckendorf.pdf\">Algorithm for identification and sequencing of protein variants using top-down MS data<\/a><\/strong><\/b><br \/>\nChristian Heckendorf, Roger Theberge, Jean L. Spencer, Catherine E. Costello, and Mark E. McComb, <b><strong>ASMS 2013<\/strong><\/b>, Minneapolis, MN.<\/span><\/li>\n<\/ul>\n<ul>\n<li><span><b><strong><a href=\"\/msr\/files\/2016\/11\/ASMS-2012-BUPID-Heckendorf.pdf\">Development of a web-based top-down protein identification tool<\/a><\/strong><\/b><br \/>\nChristian Heckendorf, Roger Theberge, Catherine E. Costello, and Mark E. McComb, <b><strong>ASMS 2012<\/strong><\/b>, Vancouver, BC.<\/span><\/li>\n<\/ul>\n<ul>\n<li><span><b><strong><a href=\"\/msr\/files\/2016\/11\/ASMS-2011-BUPID-Heckendorf.pdf\">Development of a web-based top-down data analysis tool<\/a><\/strong><\/b><br \/>\nChristian Heckendorf, Roger Theberge, Catherine E. Costello, and Mark E. McComb, <b><strong>ASMS 2011<\/strong><\/b>, Denver, CO.<\/span><\/li>\n<\/ul>\n<ul>\n<li><span><b><strong><a href=\"\/msr\/files\/2016\/11\/ASMS-2009-BUPID-Tong.pdf\">BUPID-Top-Down: Database search and assignment of top-down MS-MS data<\/a><\/strong><\/b><br \/>\nWeiwei Tong, Roger Theberge, Giuseppe Infusini, David H. Perlman, Catherine E. Costello, and Mark E. McComb, <b><strong>ASMS 2009<\/strong><\/b>, Philadelphia, PA.<\/span><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>BUPID Top-Down: Software Tools for Analysis of Top-Down MS\/MS Spectra BUPID (Boston University Protein Identifier) Top-Down is a web-based platform developed at the Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA). The platform provides the means to analyze top-down MS\/MS spectra obtained with a number of fragmentation methods, including CID, ECD, and [&hellip;]<\/p>\n","protected":false},"author":12815,"featured_media":0,"parent":1457,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2769"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/users\/12815"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/comments?post=2769"}],"version-history":[{"count":7,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2769\/revisions"}],"predecessor-version":[{"id":3196,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2769\/revisions\/3196"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/1457"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/media?parent=2769"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}