{"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":"2023-04-18T09:30:15","modified_gmt":"2023-04-18T09:30:15","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\u00a0cells<\/li>\n\n\n\n<li>Microbial pellet: 5-25 mg<\/li>\n\n\n\n<li>Tissue: 5-25 mg<\/li>\n\n\n\n<li>Biofluids (plasma\/ serum and urine): 50 \u03bcL<\/li>\n<\/ul>\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, additives, buffers and MilliQ nanopure water<\/li>\n\n\n\n<li>Avoid contact with any plastic material during lipid extractions. Use glassware and glass syringes during lipid extraction.<\/li>\n\n\n\n<li>The following plasticware can be used if required:\n<ul class=\"wp-block-list\">\n<li>Eppendorf Safe-Lock Tubes, 2.0 mL (Part number 0030120094)<\/li>\n\n\n\n<li>Eppendorf Safe-Lock Tubes, 1.5 mL (Part number 0030120086)<\/li>\n\n\n\n<li>Eppendorf\u00ae twin-tec PCR plates 96 eppendorf (Part number Z651486)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Use clean containers, sample tubes, Eppendorf tubes for sample processing and storage<\/li>\n\n\n\n<li>Avoid glassware that has been cleaned with detergent e.g. from the EMBL kitchen, or clean them several times with MilliQ water and MS-grade organic solvents prior to usage.<\/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 \/ under nitrogen (preferred at cool conditions or room temperature)<\/li>\n\n\n\n<li>Aqueous methanolic extracts<\/li>\n\n\n\n<li>For outstations: please ship samples in sufficient dry ice.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Recommended reconstitution solvents<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Water (50\u250080%)<\/li>\n\n\n\n<li>Aqueous methanol\/acetonitrile (20\u250080%)<\/li>\n\n\n\n<li>Isopropanol<\/li>\n\n\n\n<li>Methanol (caution: volume changes due to solvent evaporation at room temperature)<\/li>\n\n\n\n<li>Minimum reconstitution volume 50-100 \u03bcl<\/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>Do include pooled QC samples with each batch of samples for bracketing during analysis.<\/li>\n\n\n\n<li>Internal standards spiking during sample preparation: Deuterated or 13C internal standards are an ideal choice.<\/li>\n\n\n\n<li>Prepare replicates, preferentially biological and preparation replicates<\/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\">Before sample submission, make sure that:<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>extracts are completely soluble reconstitution solvents<\/li>\n\n\n\n<li>samples are centrifuged above 10,000 g<\/li>\n\n\n\n<li>there is no insoluble matter in samples<\/li>\n\n\n\n<li>extracts are filtered if necessary (make sure to wash filters prior to usage, as some filter membranes contain stabilizing reagents)<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Storage<\/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 would help to prevent oxidation)<\/li>\n\n\n\n<li>During processing, samples should be kept on ice<\/li>\n\n\n\n<li>Pack samples in dry ice for shipment times of more than 1 hour<\/li>\n\n\n\n<li>Samples will be kept at 4\u00b0C during LC-MS analysis<\/li>\n<\/ul>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[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":4,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/pages\/112\/revisions"}],"predecessor-version":[{"id":7240,"href":"https:\/\/www.embl.org\/groups\/metabolomics\/wp-json\/wp\/v2\/pages\/112\/revisions\/7240"}],"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}]}}