{"id":2760,"date":"2016-11-10T13:36:48","date_gmt":"2016-11-10T18:36:48","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/msr\/?page_id=2760"},"modified":"2016-11-10T13:44:26","modified_gmt":"2016-11-10T18:44:26","slug":"quick-start","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/msr\/software\/strap\/quick-start\/","title":{"rendered":"Quick Start"},"content":{"rendered":"<h3><strong>Setup Page<\/strong><\/h3>\n<ul>\n<li>Enter data files by group (maximum 4 groups): For each group, click \u201cAdd Group,\u201d type group name, and click \u201cOK.\u201d Navigate to directory, select files in group (maximum 10 files), and click \u201cOpen.\u201d<\/li>\n<li>Enter parameters: Color Legend = \u201cSolid Colors,\u201d Peptide Probability Type = \u201cInitial,\u201d Peptide Probability Cutoff = 0.5, and Group Overlap of Proteins = 0.5 (Default).<\/li>\n<li>Download Unimod database: Click \u201cUpdate\u201d (required first time after installation).<\/li>\n<li>Enter protein sequence database: Select \u201cUniProtKB\u201d (Default) or \u201cCustom Database.\u201d For \u201cCustom Database,\u201d click \u201cBrowse \u2026,\u201d navigate to directory, select FASTA file, and click \u201cOpen.\u201d<\/li>\n<li>Enter PTM score factors: \u201cQuality,\u201d \u201cGrouping,\u201d \u201cOccupancy,\u201d and \u201cUniqueness\u201d (Default).<\/li>\n<li>Run analysis: Click \u201cCompare ProtXML Files.\u201d<\/li>\n<\/ul>\n<h3><\/h3>\n<h3><strong>Results Page<\/strong><\/h3>\n<ul>\n<li>View protein information: Protein Summary (upper left panel), Global PTMs (lower left panel), and PTM Map (click \u201cPTM Map\u201d tab at bottom).<strong><\/strong><\/li>\n<li>View peptide information: Peptide Summary (click \u201cPeptide Information\u201d tab at bottom), Peptide Summary Statistics (click \u201cPeptide Information\u201d tab at bottom), Peptide PTM Summary (click \u201cPeptide Information\u201d tab at bottom, and click \u201cPeptide PTM Summary\u201d tab at upper right), and Peptide PTM Details (click \u201cPeptide Information\u201d tab at bottom, and click \u201cPeptide PTM Details\u201d tab at upper right).<\/li>\n<li>View PTM information: Summary of PTMs on Protein (click \u201cPTM Overview\u201d tab at bottom).<\/li>\n<li>Redo analysis: Click \u201cSetup\u201d tab at lower left, make changes, and rerun analysis.<\/li>\n<li>Help: <strong><a href=\"https:\/\/www.bumc.bu.edu\/msr\/contact-us\/\" title=\"Contact Us\">Contact Us<\/a><\/strong><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Setup Page Enter data files by group (maximum 4 groups): For each group, click \u201cAdd Group,\u201d type group name, and click \u201cOK.\u201d Navigate to directory, select files in group (maximum 10 files), and click \u201cOpen.\u201d Enter parameters: Color Legend = \u201cSolid Colors,\u201d Peptide Probability Type = \u201cInitial,\u201d Peptide Probability Cutoff = 0.5, and Group Overlap [&hellip;]<\/p>\n","protected":false},"author":12815,"featured_media":0,"parent":2689,"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\/2760"}],"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=2760"}],"version-history":[{"count":1,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2760\/revisions"}],"predecessor-version":[{"id":2761,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2760\/revisions\/2761"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2689"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/media?parent=2760"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}