{"id":52,"date":"2020-06-16T17:44:49","date_gmt":"2020-06-16T17:44:49","guid":{"rendered":"https:\/\/www.embl.org\/groups\/proteomics\/?page_id=52"},"modified":"2025-11-05T10:44:42","modified_gmt":"2025-11-05T10:44:42","slug":"protocols","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/proteomics\/protocols\/","title":{"rendered":"Protocols"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-4\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">SDS-PAGE &amp; Coomassie-staining<\/h2>\n\n<\/div>\n<\/div>\n\n\n<div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>We only perform processing of gel bands stained with Coomassie. Therefore, please ensure your Coomassie stain is <strong>MS-compatible<\/strong> by consulting the manufacturer\u2019s datasheet or contacting their customer service. If you want to mix your own staining solution, please see protocol on the right for a compatible recipe. <\/p>\n\n\n\n<p><strong>Important information<\/strong>:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Do not boil or microwave your gel. <br>This will impair the analysis of your protein by fixing it in the gel.<\/li>\n\n\n\n<li>Never use overhead projector foils for gel scanning. <\/li>\n<\/ul>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"768\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/CoomassieBottle_v2-1024x768.png\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/CoomassieBottle_v2-1024x768.png 1024w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/CoomassieBottle_v2-300x225.png 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/CoomassieBottle_v2-768x576.png 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/CoomassieBottle_v2.png 1200w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2020\/06\/coomassie_staining.pdf\">\n      Colloidal Coomassie Staining       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n            <p class=\"vf-card__subheading\">Protocol<\/p>\n          <\/div>\n<\/article>\n\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<div class=\"vf-grid | vf-grid__col-4\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">Submission of excised gel bands<\/h2>\n\n<\/div>\n<\/div>\n\n\n<div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p><span style=\"text-decoration: underline;\">For external customers<\/span>:<\/p>\n\n\n\n<p>When submitting gels from outside EMBL Heidelberg, we prefer that you send already excised gel bands. This will minimize the risk that your sample(s) will get damaged during transport.<\/p>\n\n\n\n<p>Please refer to the protocol on the right to excise the gel bands.<\/p>\n\n\n\n<p><span style=\"text-decoration: underline;\">For customers from EMBL Heidelberg<\/span>:<\/p>\n\n\n\n<p>You can bring your gel to our facility after destaining.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"768\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/Gel-Excised-1-1024x768.png\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/Gel-Excised-1-1024x768.png 1024w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/Gel-Excised-1-300x225.png 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/Gel-Excised-1-768x576.png 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/Gel-Excised-1.png 1200w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/Excision-of-gel-bands.pdf\">\n      Excision of Gel Bands       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n            <p class=\"vf-card__subheading\">Protocol<\/p>\n          <\/div>\n<\/article>\n\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<div class=\"vf-grid | vf-grid__col-4\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">Tryptophan assay<\/h2>\n\n<\/div>\n<\/div>\n\n\n<div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>Based on the method described by Wi\u015bniewski and Gaugaz (<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/ac504689z\">DOI: 10.1021\/ac504689z<\/a>), this fluorescence-based assay is cost-effective, user-friendly, and compatible with a wide range of sample types and buffer components.<br><em>Note: This assay requires <strong>black microplates<\/strong> and a <strong>fluorescence<\/strong>-capable <strong>plate reade<\/strong>r. Please check compatibility with your equipment.<\/em><\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"768\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/tryptophane-assay-1024x768.png\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/tryptophane-assay-1024x768.png 1024w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/tryptophane-assay-300x225.png 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/tryptophane-assay-768x576.png 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/tryptophane-assay.png 1200w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/10\/EMBL_ProteomicsCoreFacility_WFAssay.pdf\">\n      Tryptophan assay       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n            <p class=\"vf-card__subheading\">Protocol<\/p>\n          <\/div>\n<\/article>\n\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<div class=\"vf-grid | vf-grid__col-4\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">Cell lysis<\/h2>\n\n<\/div>\n<\/div>\n\n\n<div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>This protocol describes a simple and efficient <strong>denaturing lysis<\/strong> method for <strong>mammalian<\/strong> cells. It is intended as a general option when no project-specific protocol is available.<\/p>\n\n\n\n<p>If you are uncertain whether this procedure is suitable for your experimental setup or research question, please <a href=\"mailto:pcf@embl.de\">contact us<\/a> for guidance.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"640\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/11\/Cell-lysis2-1024x640.png\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/11\/Cell-lysis2-1024x640.png 1024w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/11\/Cell-lysis2-300x188.png 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/11\/Cell-lysis2-768x480.png 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/11\/Cell-lysis2-1536x960.png 1536w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/11\/Cell-lysis2-2048x1280.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/11\/Lysis-Protocol_MammalianCells.pdf\">\n      Mammalian cell lysis       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n            <p class=\"vf-card__subheading\">Protocol<\/p>\n          <\/div>\n<\/article>\n\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":3,"featured_media":0,"parent":0,"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-52","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/pages\/52","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/comments?post=52"}],"version-history":[{"count":56,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/pages\/52\/revisions"}],"predecessor-version":[{"id":26059,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/pages\/52\/revisions\/26059"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/media?parent=52"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/embl_taxonomy?post=52"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}