{"id":2708,"date":"2016-11-09T15:10:04","date_gmt":"2016-11-09T20:10:04","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/msr\/?page_id=2708"},"modified":"2016-11-09T17:19:48","modified_gmt":"2016-11-09T22:19:48","slug":"quick-start","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/msr\/software\/strap-ptm\/quick-start\/","title":{"rendered":"Quick Start"},"content":{"rendered":"<h3><strong>Setup Page<\/strong><\/h3>\n<ul>\n<li style=\"text-align: justify;\">Enter data files by group (maximum 4 groups):\u00a0 For each group, click &#8220;Add Group,&#8221; type group name, and click &#8220;OK.&#8221;\u00a0 Navigate to directory, select files in group (maximum 10 files), and click &#8220;Open.&#8221;<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">Enter parameters:\u00a0 Color Legend = &#8220;Solid Colors,&#8221; Peptide Probability Type = &#8220;Initial,&#8221; Peptide Probability Cutoff = 0.5, and Group Overlap of Proteins = 0.5 (Default).<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">Download Unimod database:\u00a0 Click &#8220;Update&#8221; (required first time after installation).<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">Enter protein sequence database:\u00a0 Select &#8220;UniProtKB&#8221; (Default) or &#8220;Custom Database.&#8221;\u00a0 For &#8220;Custom Database,&#8221; click &#8220;Browse &#8230;,&#8221; navigate to directory, select FASTA file, and click &#8220;Open.&#8221;<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">Enter PTM score factors:\u00a0 &#8220;Quality,&#8221; &#8220;Grouping,&#8221; &#8220;Occupancy,&#8221; and &#8220;Uniqueness&#8221; (Default).<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">Run analysis:\u00a0 Click &#8220;Compare ProtXML Files.&#8221;<\/li>\n<\/ul>\n<h3 style=\"text-align: justify;\"><\/h3>\n<h3 style=\"text-align: justify;\"><strong>Results Page<\/strong><\/h3>\n<ul>\n<li style=\"text-align: justify;\">View protein information:\u00a0 Protein Summary (upper left panel), Global PTMs (lower left panel), and PTM Map (click &#8220;PTM Map&#8221; tab at bottom).<strong> <\/strong><\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">View peptide information:\u00a0 Peptide Summary (click &#8220;Peptide Information&#8221; tab at bottom), Peptide Summary Statistics (click &#8220;Peptide Information&#8221; tab at bottom), Peptide PTM Summary (click &#8220;Peptide Information&#8221; tab at bottom, and click &#8220;Peptide PTM Summary&#8221; tab at upper right), and Peptide PTM Details (click &#8220;Peptide Information&#8221; tab at bottom, and click &#8220;Peptide PTM Details&#8221; tab at upper right).<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">View PTM information:\u00a0 Summary of PTMs on Protein (click &#8220;PTM Overview&#8221; tab at bottom).<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">Redo analysis:\u00a0 Click &#8220;Setup&#8221; tab at lower left, make changes, and rerun analysis.<\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\">Help:\u00a0 <strong><a href=\"https:\/\/www.bumc.bu.edu\/msr\/contact-us\/\" title=\"Contact Us\">Contact Us<\/a><\/strong><\/li>\n<\/ul>\n<ul><\/ul>\n<p><!-- [if gte mso 9]&gt;     &lt;![endif]--><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Setup Page Enter data files by group (maximum 4 groups):\u00a0 For each group, click &#8220;Add Group,&#8221; type group name, and click &#8220;OK.&#8221;\u00a0 Navigate to directory, select files in group (maximum 10 files), and click &#8220;Open.&#8221; Enter parameters:\u00a0 Color Legend = &#8220;Solid Colors,&#8221; Peptide Probability Type = &#8220;Initial,&#8221; Peptide Probability Cutoff = 0.5, and Group Overlap [&hellip;]<\/p>\n","protected":false},"author":12815,"featured_media":0,"parent":2683,"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\/2708"}],"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=2708"}],"version-history":[{"count":3,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2708\/revisions"}],"predecessor-version":[{"id":2742,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2708\/revisions\/2742"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2683"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/media?parent=2708"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}