{"id":209,"date":"2025-03-02T02:14:56","date_gmt":"2025-03-02T02:14:56","guid":{"rendered":"https:\/\/wpdev.acsu.buffalo.edu\/virtualglycome\/?page_id=209"},"modified":"2025-03-02T02:14:56","modified_gmt":"2025-03-02T02:14:56","slug":"gpannotate","status":"publish","type":"page","link":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/gpannotate\/","title":{"rendered":"GpAnnotate"},"content":{"rendered":"\n<p><code><strong><mark class=\"has-inline-color has-contrast-color\">A program for the detailed annotation of MS\/MS glycoproteomics spectra using DrawGlycan-SNFG sketches<\/mark><\/strong><\/code><\/p>\n\n\n\n<p><strong>Citation:&nbsp; &nbsp;Cheng et al. &#8216;DrawGlycan-SNFG &amp; gpAnnotate: Rendering glycans and annotating glycopeptide spectra&#8217;, Bioinformatics, 36(6):1942-43, 2020&nbsp;<a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btz819\"><u>[link].<\/u><\/a><\/strong><\/p>\n\n\n\n<p><strong>Links to:<\/strong>&nbsp; &nbsp;  <a href=\"https:\/\/virtualglycome.org\/app\/site\/media\/gpAnnotate_Manual.pdf\" target=\"_blank\" rel=\"noreferrer noopener\"><u>View&nbsp;User Manual<\/u><\/a><\/p>\n\n\n\n<p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<a href=\"https:\/\/sourceforge.net\/projects\/gpannotate\/files\/Example%20Files\/\"><u>Download user manual and test data set [.zip file].<\/u><\/a><\/p>\n\n\n\n<p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<a href=\"https:\/\/sourceforge.net\/projects\/gpannotate\/files\/Standalone\/v1.0\/\"><u>Download Compiled Program for Win\/Mac\/Linux<\/u><\/a>.&nbsp;To install, download and double-click (disable anti-virus software, if necessary)<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>About&nbsp;gpAnnotate<\/strong><\/h2>\n\n\n\n<p>The Glycopeptide Spectrum Annotation program (<strong>gpAnnotate<\/strong>) is designed to annotate individual glycoproteomics MS\/MS spectrum for several established mass spectrometry&nbsp;fragmentation modes:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>CID<\/strong>: collision induced dissociation<\/li>\n\n\n\n<li><strong>HCD<\/strong>: beam-type CID or higher-energy collision dissociation<\/li>\n\n\n\n<li><strong>ETD<\/strong>: electron transfer dissociation<\/li>\n\n\n\n<li><strong>ETciD<\/strong>: electron-transfer-CID, and<\/li>\n\n\n\n<li><strong>EThcD<\/strong>: electron-transfer-HCD.<\/li>\n<\/ul>\n\n\n\n<p>In addition to preset options that are fixed for the above modes, gpAnnotate also allows \u2018<strong>Custom<\/strong>\u2019 definition of fragmentation rules in order to accommodate additional user preferences. Thus, in principle, it can handle a wide variety of scenarios.<\/p>\n\n\n\n<p>A key feature of the program is the use of\u00a0<a href=\"http:\/\/www.virtualglycome.org\/DrawGlycan\/\">DrawGlycan-SNFG<\/a>\u00a0(version 2,\u00a0<strong>[ref. 1]<\/strong>) for the annotation of MS\/MS spectrum. Many of the scoring algorithms incorporated into gpAnnotate are derived from the GlycoProteomics Analysis ToolBox (<a href=\"https:\/\/virtualglycome.org\/glycopat\/\">GlycoPAT<\/a>,\u00a0<strong>[ref. 2]<\/strong>). Additional updates to GlycoPAT for large scale glycoproteomics studies will be released shortly (manuscript in preparation).\u00a0<\/p>\n\n\n\n<p>gpAnnotate includes 3 modules. The main&nbsp;GUI (graphical user interface) interface is shown below along with the interfaces for: i. Preprocessing of experimental data;&nbsp;ii. Annotating&nbsp;of MS\/MS spectrum; and&nbsp;iii. DrawGlycan-SNFG (version 2). A sample output GUI is also shown.<\/p>\n\n\n\n<p>Instructions for software installation, technical details and usage directions are provided in the program manual. A separate website is also available for&nbsp;<a href=\"http:\/\/www.virtualglycome.org\/DrawGlycan\/\">DrawGlycan-SNFG<\/a>.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>To test gpAnnotate<\/strong>:&nbsp;<\/h2>\n\n\n\n<p class=\"has-accent-3-color has-text-color has-link-color wp-elements-f416d7a37b0d9cfc3f9828b8494cd7e6\">Download the&nbsp;<a href=\"https:\/\/sourceforge.net\/projects\/gpannotate\/files\/Standalone\/\">gpAnnotate standalone application<\/a>&nbsp;and&nbsp;<a href=\"https:\/\/sourceforge.net\/projects\/gpannotate\/files\/Example%20Files\/\">example files<\/a>&nbsp;using the above link.<\/p>\n\n\n\n<p>i. Select one of the example data files (either &#8220;testdata_cryo.mat&#8221; or &#8220;testdata_mix.mat&#8221;);<\/p>\n\n\n\n<p>ii. Copy scan number and glycopeptide SGP sequence from &#8220;Example_Candidates_and_Results.xlsx&#8221; to the corresponding boxes in the software interface;<\/p>\n\n\n\n<p>iii. Hit &#8220;Annotate&#8221; to run the program.<\/p>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/virtualglycome.org\/app\/site\/media\/gpAnnotateFig.jpg\" alt=\"\" title=\"GUI interfaces of gpAnnotate\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/virtualglycome.org\/app\/site\/media\/output.jpg\" alt=\"\" title=\"Sample output from gpAnnotate\" \/><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>References<\/strong>:<\/h2>\n\n\n\n<p>1.&nbsp; &nbsp; Cheng, K., Y. Zhou, and S. Neelamegham,&nbsp;<em>DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information.<\/em>&nbsp;Glycobiology, 2017.&nbsp;<strong>27<\/strong>(3): p. 200-205.<\/p>\n\n\n\n<p>2.&nbsp;&nbsp;&nbsp;&nbsp;Liu, G., et al.,&nbsp;<em>A Comprehensive, Open-source Platform for Mass Spectrometry-based Glycoproteomics Data Analysis.<\/em>&nbsp;Mol Cell Proteomics, 2017.&nbsp;<strong>16<\/strong>(11): p. 2032-2047.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A program for the detailed annotation of MS\/MS glycoproteomics spectra using DrawGlycan-SNFG sketches Citation:&nbsp; &nbsp;Cheng et al. &#8216;DrawGlycan-SNFG &amp; gpAnnotate: Rendering glycans and annotating glycopeptide spectra&#8217;, Bioinformatics, 36(6):1942-43, 2020&nbsp;[link]. Links [&hellip;]<\/p>\n","protected":false},"author":617,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_EventAllDay":false,"_EventTimezone":"","_EventStartDate":"","_EventEndDate":"","_EventStartDateUTC":"","_EventEndDateUTC":"","_EventShowMap":false,"_EventShowMapLink":false,"_EventURL":"","_EventCost":"","_EventCostDescription":"","_EventCurrencySymbol":"","_EventCurrencyCode":"","_EventCurrencyPosition":"","_EventDateTimeSeparator":"","_EventTimeRangeSeparator":"","_EventOrganizerID":[],"_EventVenueID":[],"_OrganizerEmail":"","_OrganizerPhone":"","_OrganizerWebsite":"","_VenueAddress":"","_VenueCity":"","_VenueCountry":"","_VenueProvince":"","_VenueState":"","_VenueZip":"","_VenuePhone":"","_VenueURL":"","_VenueStateProvince":"","_VenueLat":"","_VenueLng":"","_VenueShowMap":false,"_VenueShowMapLink":false,"footnotes":""},"class_list":["post-209","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/wp-json\/wp\/v2\/pages\/209","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/wp-json\/wp\/v2\/users\/617"}],"replies":[{"embeddable":true,"href":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/wp-json\/wp\/v2\/comments?post=209"}],"version-history":[{"count":0,"href":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/wp-json\/wp\/v2\/pages\/209\/revisions"}],"wp:attachment":[{"href":"https:\/\/ubwp.buffalo.edu\/virtualglycome\/wp-json\/wp\/v2\/media?parent=209"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}