{"id":180,"date":"2026-04-10T15:43:07","date_gmt":"2026-04-10T15:43:07","guid":{"rendered":"https:\/\/site.uvm.edu\/alca\/?page_id=180"},"modified":"2026-07-01T13:29:27","modified_gmt":"2026-07-01T13:29:27","slug":"gcms","status":"publish","type":"page","link":"https:\/\/site.uvm.edu\/alca\/instrumentation\/gcms\/","title":{"rendered":"Gas Chromatography &#8211; Mass Spectrometer (GC-MS)"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">The Agilent 5977B GC\/MSD System coupled with an Agilent 8860 Gas Chromatograph provides robust analysis of volatile and semi-volatile organic compounds. Gas chromatography enables high-resolution separation, while electron ionization (EI) produces reproducible fragmentation patterns for compound identification.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The system is well-suited for both targeted and unknown analysis, with extensive spectral library matching capabilities for confident compound identification.<\/p>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-adc57f8e wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-group has-global-padding is-layout-constrained wp-block-group-is-layout-constrained\">\n<h2 class=\"wp-block-heading has-primary-uvmgreen-color has-text-color has-link-color wp-elements-e45775b91bd0c519d5de4e8bb3bad256\">Modes of Operations<\/h2>\n<\/div>\n\n\n\n<div class=\"wp-block-group has-global-padding is-layout-constrained wp-block-group-is-layout-constrained\">\n<div class=\"wp-block-group has-global-padding is-layout-constrained wp-block-group-is-layout-constrained\">\n<h3 class=\"wp-block-heading\">Full Scan MS (High-Resolution)<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Accurate mass measurements across a wide m\/z range of 0.6 &#8211; 1091<\/li>\n\n\n\n<li>Used for:\n<ul class=\"wp-block-list\">\n<li>Unknown identification<\/li>\n\n\n\n<li>Library matching<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<h2 class=\"wp-block-heading has-primary-uvmgreen-color has-text-color has-link-color wp-elements-72f25bf3fc8e76abdfb5bdb31660c947\">Ionization Modes<\/h2>\n\n\n\n<div class=\"wp-block-group has-global-padding is-layout-constrained wp-block-group-is-layout-constrained\">\n<h3 class=\"wp-block-heading\">Electron Ionization (EI)<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Hard ionization at 70eV<\/li>\n\n\n\n<li>Produces reproducible fragmentation patterns<\/li>\n\n\n\n<li><strong>Key advantages<\/strong>\n<ul class=\"wp-block-list\">\n<li>Extensive spectral libraries (e.g. NIST)<\/li>\n\n\n\n<li>Highly reliable compound identification<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-align-center has-primary-uvmgreen-color has-text-color has-link-color wp-elements-63de3437f2c801e3d096e10f7056ca73\">Current Instrument Setup<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">System Configuration<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Gas Chromatograph: Agilent 8860 Gas Chromatograph<\/li>\n\n\n\n<li>Mass Spectrometer: Agilent 5977B MSD<\/li>\n\n\n\n<li>Autosampler: 16-position for automated sample injection<\/li>\n\n\n\n<li>Software Platforms: MassHunter<\/li>\n\n\n\n<li>Data Analysis: MassHunter Qualitative Analysis<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Column Configuration<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>HP-5MS column (30 m x 0.25 mm x 0.25\u00b5m) <\/li>\n\n\n\n<li>Stationary Phase:\n<ul class=\"wp-block-list\">\n<li>(5%-phenyl)-methylpolysiloxane<\/li>\n\n\n\n<li>Low polarity column<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>What this means practically\n<ul class=\"wp-block-list\">\n<li>Broad applicability across a wide range of organic compounds<\/li>\n\n\n\n<li>Good Separation of:\n<ul class=\"wp-block-list\">\n<li>Volatile organic compounds (VOCs)<\/li>\n\n\n\n<li>Semi-volatile compounds (SVOCs)<\/li>\n\n\n\n<li>Aromatics and hydrocarbons<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Alternative Detector<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Flame Ionization Detector (FID)<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The GC system is equipped with a&nbsp;<strong>FID<\/strong> which provides highly sensitive and quantitative detection of hydrocarbons and organic compounds.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The FID is&nbsp;<strong>not currently in routine operation<\/strong>&nbsp;due to gas supply requirements. Activation of this detector may be considered based on user demand and project needs.<\/p>\n\n\n\n<div class=\"wp-block-group has-global-padding is-layout-constrained wp-block-group-is-layout-constrained\">\n<h2 class=\"wp-block-heading has-text-align-center has-primary-uvmgreen-color has-text-color has-link-color wp-elements-bb852d8247b1f0954506804a62f69aa5\">Sample Requirements <\/h2>\n\n\n\n<h4 class=\"wp-block-heading\">Sample Prep<\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Samples should be <strong>fully dissolved in<\/strong> <strong>most organic solvents <\/strong>\n<ul class=\"wp-block-list\">\n<li>Preferred:\n<ul class=\"wp-block-list\">\n<li>acetone, methanol, hexane, aromatics, and alkanes<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Less preferable:\n<ul class=\"wp-block-list\">\n<li>Halogenated solvents (e.g chloroform, methylene chloride, etc.) <\/li>\n\n\n\n<li>Ethers (diethyl ether, THF, etc)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Do Not Use<\/strong>:\n<ul class=\"wp-block-list\">\n<li>Water<\/li>\n\n\n\n<li>DMSO<\/li>\n\n\n\n<li>DMF<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Concentration<\/strong> <strong>Guidelines<\/strong>\n<ul class=\"wp-block-list\">\n<li>Solutions should be submitted approximately 10 ug\/mL in a solvent suitable for GC-MS<\/li>\n\n\n\n<li>Do not use overly concentrated samples (&gt;1.0 mg\/mL) as it can damage the detector<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Liquid Samples \n<ul class=\"wp-block-list\">\n<li>Should not contain any particles or precipitates that will block the syringe<\/li>\n\n\n\n<li><strong>Centrifuge or Filter samples <\/strong>prior <\/li>\n\n\n\n<li><strong>If starting from aqueous samples<\/strong>\n<ul class=\"wp-block-list\">\n<li>Preform liquid-liquid extraction (LLE) into an organic solvent <\/li>\n\n\n\n<li>Or use solid-phase extraction (SPE)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Avoid<\/strong> (Some classes of compounds are not amenable to GC-MS analysis and should not be used)\n<ul class=\"wp-block-list\">\n<li>Strong Acids\/Bases<\/li>\n\n\n\n<li>Salts<\/li>\n\n\n\n<li>Metals<\/li>\n\n\n\n<li>Polymeric materials<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">Sample Cleanliness<\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Filter samples using <strong>0.2 \u00b5m or 0.45 \u00b5m filters<\/strong> or alternatively centrifuge to remover particles <\/li>\n\n\n\n<li>Particles can \n<ul class=\"wp-block-list\">\n<li>Clog the syringe<\/li>\n\n\n\n<li>Damage the column<\/li>\n\n\n\n<li>Affect reproducibility<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-align-center has-primary-uvmgreen-color has-text-color has-link-color wp-elements-4c85efac5d18e729f8830f671bdb74b4\">Rates<\/h2>\n\n\n\n<figure class=\"wp-block-table is-style-stripes is-style-stripes--1\"><table class=\"has-fixed-layout\"><thead><tr><th class=\"has-text-align-center\" data-align=\"center\">Service (per hour)<\/th><th class=\"has-text-align-center\" data-align=\"center\">UVM Users<\/th><th class=\"has-text-align-center\" data-align=\"center\">External Users<\/th><\/tr><\/thead><tbody><tr><td class=\"has-text-align-center\" data-align=\"center\">User Instrument Time<\/td><td class=\"has-text-align-center\" data-align=\"center\">$31.75<\/td><td class=\"has-text-align-center\" data-align=\"center\">$47.62<\/td><\/tr><tr><td class=\"has-text-align-center\" data-align=\"center\">Staff Assisted Use<\/td><td class=\"has-text-align-center\" data-align=\"center\">$101.02<\/td><td class=\"has-text-align-center\" data-align=\"center\">$151.53<\/td><\/tr><tr><td class=\"has-text-align-center\" data-align=\"center\">Training Session<\/td><td class=\"has-text-align-center\" data-align=\"center\">$101.02<\/td><td class=\"has-text-align-center\" data-align=\"center\">$151.53<\/td><\/tr><\/tbody><tfoot><tr><td class=\"has-text-align-center\" data-align=\"center\">Prices as of July 1, 2026<\/td><td class=\"has-text-align-center\" data-align=\"center\"><\/td><td class=\"has-text-align-center\" data-align=\"center\"><\/td><\/tr><\/tfoot><\/table><\/figure>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-adc57f8e wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<h3 class=\"wp-block-heading has-text-align-center has-primary-uvmgreen-color has-text-color has-link-color wp-elements-fbc6f45e5064b4a755f9026bba77c833\">Training<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Interested in using the GC-MS independently?<\/strong><br>Schedule training to learn instrument operation, method setup, and data analysis using spectral libraries.<\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<h3 class=\"wp-block-heading has-text-align-center has-primary-uvmgreen-color has-text-color has-link-color wp-elements-81cf02e4f1bc8ebb8729caa940f0a538\">Analysis<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Need help analyzing samples?<\/strong><br>Submit samples for full-service GC-MS analysis, including method development, data acquisition, and compound identification.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-buttons is-layout-flex wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button has-custom-width wp-block-button__width-50\"><a class=\"wp-block-button__link has-white-color has-primary-uvmgreen-background-color has-text-color has-background has-link-color wp-element-button\" href=\"https:\/\/site.uvm.edu\/alca\/contact\/\">Schedule Training<\/a><\/div>\n\n\n\n<div class=\"wp-block-button has-custom-width wp-block-button__width-50\"><a class=\"wp-block-button__link has-primary-uvmgreen-background-color has-background wp-element-button\" href=\"https:\/\/uvm.ilab.agilent.com\/service_center\/show_external\/6442?name=laboratory-for-chemical-analysis\">Request Analysis on iLabs<\/a><\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>The Agilent 5977B GC\/MSD System coupled with an Agilent 8860 Gas Chromatograph provides robust analysis of volatile and semi-volatile organic compounds. Gas chromatography enables high-resolution separation, while electron ionization (EI) produces reproducible fragmentation patterns for compound identification. The system is well-suited for both targeted and unknown analysis, with extensive spectral library matching capabilities for confident [&hellip;]<\/p>\n","protected":false},"author":10857,"featured_media":217,"parent":20,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-180","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/pages\/180","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/users\/10857"}],"replies":[{"embeddable":true,"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/comments?post=180"}],"version-history":[{"count":18,"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/pages\/180\/revisions"}],"predecessor-version":[{"id":462,"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/pages\/180\/revisions\/462"}],"up":[{"embeddable":true,"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/pages\/20"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/media\/217"}],"wp:attachment":[{"href":"https:\/\/site.uvm.edu\/alca\/wp-json\/wp\/v2\/media?parent=180"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}