{"id":33977,"date":"2023-04-25T10:19:14","date_gmt":"2023-04-25T14:19:14","guid":{"rendered":"https:\/\/web.uri.edu\/riinbre\/?p=33977"},"modified":"2023-09-07T09:16:17","modified_gmt":"2023-09-07T13:16:17","slug":"mass_spec_proteomics_wdt23","status":"publish","type":"post","link":"https:\/\/web.uri.edu\/riinbre\/mass_spec_proteomics_wdt23\/","title":{"rendered":"Mass-Spec Proteomics and Data Analysis (WDT 2023)"},"content":{"rendered":"<h1>RI-INBRE Workforce Development Training (WDT) Summer 2023 Syllabus<\/h1>\n<h2>Module Title: Proteomics<\/h2>\n<h3>Instructor: Joseph Schrader, PhD<\/h3>\n<h3>Course Overview<\/h3>\n<p>This WDT Module aims to train students in proteomic analysis using the Sequential Acquisition of All Theoretical Mass-spectra (SWATH-MA) method. The module will include lectures on protein MS methods, hands-on laboratory experience with sample prep and analysis, and post-run data processing\/presentation. The module is intended for students new to proteomics data generation and analysis and will provide sufficient background for students to pursue further training in these and related research areas. This module also complements the separate module on genomic data generation and sequencing. The module will be completed over 2.5<br \/>\ndays and participants who complete the module will receive an RI-INBRE Certificate of Completion.<\/p>\n<h2>Learning Outcomes<\/h2>\n<ul>\n<li>Learn background on protein-MS methods sufficient to understand basic sequencing<br \/>\ntechniques and terminology.<\/li>\n<li>Prepare animal tissue samples for proteomic analysis on a Thermo Fisher Exploris 240<br \/>\nOrbitrap mass spectrometer<\/li>\n<li>Learn basic operation of mass spectrometer.<\/li>\n<li>Process LC-MS\/MS data using hands-on learning modules, using both example data and<br \/>\n(if time permits) data generated by the participants.<br \/>\no Total protein approach conversion<br \/>\no Disease model specific protein expression changes<\/li>\n<li>Analyze proteomics data using established methods such as differential expression<br \/>\nanalysis and pathway analysis<\/li>\n<\/ul>\n<h2>Lab Report<\/h2>\n<p>Students will be expected to maintain detailed laboratory notes to include:<\/p>\n<ul>\n<li>Sample preparation and digestion protocols<\/li>\n<li>Data processing\/analysis protocols (e.g., workflows, software used, etc.)<\/li>\n<li>Results of bioinformatics analysis (differential expression, pathway analysis)<\/li>\n<\/ul>\n<h2>Resources Used in this Module:<\/h2>\n<ul>\n<li>Spectronaut Biognosys Manual<\/li>\n<li>Standard Operating Procedure \u2013 Sample Preparation and MS operation<\/li>\n<li>Lab Notebooks for Hands-On Analysis<\/li>\n<li>Slide Decks for Lectures<\/li>\n<\/ul>\n<h2>Timeline<\/h2>\n\n<table id=\"tablepress-16\" class=\"tablepress tablepress-id-16\">\n<thead>\n<tr class=\"row-1\">\n\t<td class=\"column-1\"><\/td><th class=\"column-2\">Day 1<\/th><th class=\"column-3\">Day 2<\/th><th class=\"column-4\">Day 3<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-striping row-hover\">\n<tr class=\"row-2\">\n\t<td class=\"column-1\">9:00 AM-10:00 AM<\/td><td class=\"column-2\">Introduction to<br \/>\nProteomics and<br \/>\nProtein Mass<br \/>\nSpectroscopy (Lecture)<\/td><td class=\"column-3\">Introduction to Proteomics<br \/>\nData processing\/Spectronaut<br \/>\n(Lecture)<\/td><td class=\"column-4\">Data Analysis - Participant<br \/>\nSamples (Lecture\/Hands-On)<br \/>\n(con\u2019t)<\/td>\n<\/tr>\n<tr class=\"row-3\">\n\t<td class=\"column-1\">10:00 AM-11:00 AM<\/td><td class=\"column-2\">Tissue\/Cell sample<br \/>\nlysis and preparation<br \/>\nfor digestion (hands<br \/>\non)<\/td><td class=\"column-3\">Lecture continued,<br \/>\nProteomics Data Processing<br \/>\npractice data sets<br \/>\n(Lecture\/hands on)<\/td><td class=\"column-4\">Data Analysis - Participant<br \/>\nSamples (Lecture\/Hands-On)<br \/>\n(con\u2019t)<\/td>\n<\/tr>\n<tr class=\"row-4\">\n\t<td class=\"column-1\">11:00 AM-12:00 PM<\/td><td class=\"column-2\">Tissue\/Cell sample<br \/>\nlysis and preparation<br \/>\nfor digestion, pressure<br \/>\ndigestion 1 (hands on)<\/td><td class=\"column-3\">Proteomics Data Processing<br \/>\npractice data sets<br \/>\n(hands on)<\/td><td class=\"column-4\">Frontiers in Bioinformatics<br \/>\n(Open Discussion)<\/td>\n<\/tr>\n<tr class=\"row-5\">\n\t<td class=\"column-1\">12:00 - 1:00 PM<\/td><td class=\"column-2\">Break<\/td><td class=\"column-3\">Break<\/td><td class=\"column-4\">Closing Group Lunch<\/td>\n<\/tr>\n<tr class=\"row-6\">\n\t<td class=\"column-1\">1:00 PM-2:00 PM<\/td><td class=\"column-2\">Instrument<br \/>\nPreparation, pressure<br \/>\ndigestion 2 (hands on)<\/td><td class=\"column-3\">Figure preparation for data<br \/>\npresentation from (hands<br \/>\non)<\/td><td class=\"column-4\"><\/td>\n<\/tr>\n<tr class=\"row-7\">\n\t<td class=\"column-1\">2:00 PM-3:00 PM<\/td><td class=\"column-2\">Post digestion sample<br \/>\npurification<\/td><td class=\"column-3\">Spectronaut processing of<br \/>\nParticipant Samples (hands<br \/>\non)<\/td><td class=\"column-4\"><\/td>\n<\/tr>\n<tr class=\"row-8\">\n\t<td class=\"column-1\">3:00 PM-4:00 PM<\/td><td class=\"column-2\">Sample running on<br \/>\nMass spec. (hands on)<\/td><td class=\"column-3\">Data Processing\/Analysis<br \/>\nOpen discussion<\/td><td class=\"column-4\"><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-16 from cache -->\n","protected":false},"excerpt":{"rendered":"<p>RI-INBRE Workforce Development Training (WDT) Summer 2023 Syllabus Module Title: Proteomics Instructor: Joseph Schrader, PhD Course Overview This WDT Module aims to train students in proteomic analysis using the Sequential Acquisition of All Theoretical Mass-spectra (SWATH-MA) method. The module will include lectures on protein MS methods, hands-on laboratory experience with sample prep and analysis, and [&hellip;]<\/p>\n","protected":false},"author":3192,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[821],"tags":[829,830,822],"class_list":["post-33977","post","type-post","status-publish","format-standard","hentry","category-wdt2023","tag-mass-spec","tag-proteomics","tag-wdt"],"acf":[],"_links":{"self":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/33977","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/users\/3192"}],"replies":[{"embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/comments?post=33977"}],"version-history":[{"count":5,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/33977\/revisions"}],"predecessor-version":[{"id":34579,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/33977\/revisions\/34579"}],"wp:attachment":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/media?parent=33977"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/categories?post=33977"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/tags?post=33977"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}