{"id":2086,"date":"2013-06-17T23:36:15","date_gmt":"2013-06-18T03:36:15","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/?page_id=2086"},"modified":"2013-06-25T06:46:28","modified_gmt":"2013-06-25T10:46:28","slug":"quick-start","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/cpctools\/strap-ptm\/quick-start\/","title":{"rendered":"Quick Start"},"content":{"rendered":"<p><ins datetime=\"2013-06-17T02:05:02+00:00\"><img src=\"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/files\/2013\/06\/STRAPhead.png\" alt=\"straphead\" \/><\/ins><\/p>\n<h3><\/h3>\n<h3><strong>Setup Page<\/strong><\/h3>\n<ul>\n<li style=\"text-align: justify;\">Enter data files by group (maximum 4 groups):  For each group, click &#8220;Add Group,&#8221; type group name, and click &#8220;OK.&#8221;  Navigate to directory, select files in group (maximum 10 files), and click &#8220;Open.&#8221;<\/li>\n<p><\/p>\n<li style=\"text-align: justify;\">Enter parameters:  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<p><\/p>\n<li style=\"text-align: justify;\">Download Unimod database:  Click &#8220;Update&#8221; (required first time after installation).<\/li>\n<p><\/p>\n<li style=\"text-align: justify;\">Enter protein sequence database:  Select &#8220;UniProtKB&#8221; (Default) or &#8220;Custom Database.&#8221;  For &#8220;Custom Database,&#8221; click &#8220;Browse &#8230;,&#8221; navigate to directory, select FASTA file, and click &#8220;Open.&#8221;<\/li>\n<p><\/p>\n<li style=\"text-align: justify;\">Enter PTM score factors:  &#8220;Quality,&#8221; &#8220;Grouping,&#8221; &#8220;Occupancy,&#8221; and &#8220;Uniqueness&#8221; (Default).<\/li>\n<p><\/p>\n<li style=\"text-align: justify;\">Run analysis:  Click &#8220;Compare ProtXML Files.&#8221;<\/li>\n<p><\/p>\n<\/ul>\n<h3 style=\"text-align: justify;\"><\/h3>\n<h3 style=\"text-align: justify;\"><\/h3>\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:  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<p><\/p>\n<li style=\"text-align: justify;\">View peptide information:  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<p><\/p>\n<li style=\"text-align: justify;\">View PTM information:  Summary of PTMs on Protein (click &#8220;PTM Overview&#8221; tab at bottom).<\/li>\n<p><\/p>\n<li style=\"text-align: justify;\">Redo analysis:  Click &#8220;Setup&#8221; tab at lower left, make changes, and rerun analysis.<\/li>\n<p><\/p>\n<li style=\"text-align: justify;\">Help:  <strong><a href=\"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/cpctools\/strap-ptm\/contact-us\/\">Contact Us<\/a><\/strong><\/li>\n<p>\n<\/ul>\n<ul><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Setup Page Enter data files by group (maximum 4 groups): For each group, click &#8220;Add Group,&#8221; type group name, and click &#8220;OK.&#8221; Navigate to directory, select files in group (maximum 10 files), and click &#8220;Open.&#8221; Enter parameters: 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":7351,"featured_media":0,"parent":672,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/2086"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/users\/7351"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/comments?post=2086"}],"version-history":[{"count":7,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/2086\/revisions"}],"predecessor-version":[{"id":2311,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/2086\/revisions\/2311"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/672"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/media?parent=2086"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}