{"id":112,"date":"2020-06-22T10:43:24","date_gmt":"2020-06-22T10:43:24","guid":{"rendered":"https:\/\/www.embl.org\/groups\/metabolomics\/?page_id=112"},"modified":"2026-08-04T09:57:13","modified_gmt":"2026-08-04T09:57:13","slug":"guide-to-sample-cleanup-and-storage","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/metabolomics\/sample-preparation\/guide-to-sample-cleanup-and-storage\/","title":{"rendered":"Guide to sample cleanup and storage"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">General minimum amount of material required<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Cell culture: 1-2 million&nbsp;cells<\/li>\n\n\n\n<li>Microbial pellet: 5-25 mg<\/li>\n\n\n\n<li>Tissue: 5-25 mg (maximum: 50 mg)<\/li>\n\n\n\n<li>Biofluids (plasma\/ serum and urine): 20 \u03bcL<\/li>\n<\/ul>\n\n\n\n<p>Note: For solid materials, the respective weights per sample must be provided in an electronic sample list<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Recommended extraction solvents<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Metabolites: methanol, acetonitrile, water<\/li>\n\n\n\n<li>Lipids: methanol, isopropanol, MTBE<\/li>\n<\/ul>\n\n\n\n<p>Please refer to our protocols for <a href=\"https:\/\/www.embl.org\/groups\/metabolomics\/sample-preparation\/\">sample preparation<\/a> for details.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Caution:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Use only LC\/MS-grade solvents\/water, additives, and buffers<\/li>\n\n\n\n<li>Randomize the extraction order and balance all experimental groups across extraction days, batches and plates. E.g. do not process all controls first and all treated samples afterwards.<\/li>\n\n\n\n<li>Provide a processed blank sample for blank filtering (sample without biological matrix of interest)<\/li>\n\n\n\n<li>Please contact MCF staff for consultation regarding plastic laboratory tubes and sizes for your respective project<\/li>\n\n\n\n<li>Use clean containers, sample tubes, laboratory tubes for sample processing and storage<\/li>\n\n\n\n<li>Avoid glassware that has been cleaned with detergent e.g. from a laboratory kitchen. Cleaning of fresh glassware by rising multiple time with LC-MS grade solvents is required<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Samples can be submitted as:<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Dried extracts obtained using speedvac \/ blow-down nitrogen evaporators (drying preferred at cooled conditions or room temperature). Make sure to dry samples \/ supernatants after centrifugation only (at min. 10,000 g)<\/li>\n\n\n\n<li>Monophasic extracts or initial extractions for subsequent biphasic extraction<\/li>\n\n\n\n<li>Samples are to be shipped in sufficient dry ice.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Quality control<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Include pooled quality control (QC) samples (without blank samples) with each batch of samples<\/li>\n\n\n\n<li>Internal standards spiking during sample preparation: Deuterated or 13C\/15N-labelled internal standards are an ideal choice &#8211; can be provided by MCF staff<\/li>\n\n\n\n<li>Prepare biological replicates (minimum of 4 per condition are required)<\/li>\n<\/ul>\n\n\n\n<p><strong>Note:<\/strong> Please consult with MCF staff for the appropriate selection of the replicates, quality control samples, and internal standards that are suitable for your desired LC-MS analysis.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Storage &amp; Shipment<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Dried metabolite extracts should be stored at -80\u00b0C (optional filling with argon\/nitrogen can help to prevent oxidation)<\/li>\n\n\n\n<li>During processing, samples should be kept cooled (e.g. on ice)<\/li>\n\n\n\n<li>Pack samples in dry ice for shipment <\/li>\n\n\n\n<li>Use sample boxes and do not submit samples in plastic bags or just sitting on dry ice<\/li>\n\n\n\n<li>In addition to any print outs, electronic sample lists must be provided\n<ul class=\"wp-block-list\">\n<li>add all relevant metadata to the sample sheet (volume\/weight of sample; experimental group\/timepoint\/etc. per sample)<\/li>\n\n\n\n<li>add any extraction protocol performed at your site to the electronic file<\/li>\n\n\n\n<li>final reconstitution solvent and volume<\/li>\n\n\n\n<li>add information about the requested service to the sample list<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":3,"featured_media":0,"parent":106,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-112","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/pages\/112","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/comments?post=112"}],"version-history":[{"count":6,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/pages\/112\/revisions"}],"predecessor-version":[{"id":29371,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/pages\/112\/revisions\/29371"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/pages\/106"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/media?parent=112"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/embl_taxonomy?post=112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}