{"id":24119,"date":"2025-09-10T14:17:46","date_gmt":"2025-09-10T14:17:46","guid":{"rendered":"https:\/\/www.embl.org\/groups\/proteomics\/?page_id=24119"},"modified":"2025-09-25T10:52:25","modified_gmt":"2025-09-25T10:52:25","slug":"equipment","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/proteomics\/equipment\/","title":{"rendered":"Equipment"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-5\"><div class=\"vf-grid__col--span-4\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-998ab8dc-82e2-40a0-a462-a8c61966fc31\" data-vf-js-location-nearest-activation-target=\"\">Sample Preparation<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d3ac702e-be98-40ef-a5d0-8f197130092d\" data-vf-js-location-nearest-activation-target=\"\">Liquid Chromatography<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-5c164ca2-1984-4606-b311-8580756f05f7\" data-vf-js-location-nearest-activation-target=\"\">Mass Spectrometry<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-939ed7f8-9c65-48c4-8251-6e773e4ea515\" data-vf-js-location-nearest-activation-target=\"\">Data Analysis<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-998ab8dc-82e2-40a0-a462-a8c61966fc31\"><h2 class=\"vf-u-sr-only\">Sample Preparation<\/h2>\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"218\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/COL010968-King-Fisher-Apex-left-Low-Open-A-HR-300x218.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/COL010968-King-Fisher-Apex-left-Low-Open-A-HR-300x218.jpg 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/COL010968-King-Fisher-Apex-left-Low-Open-A-HR.jpg 650w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    KingFisher Apex\n    <\/h3>\n\n  <p class=\"vf-summary__text\">Semi-automated processing of samples:<\/p>\n<ul>\n<li>Sample clean-up and digestion via SP3 workflow (<a href=\"https:\/\/doi.org\/10.1038\/s41596-018-0082-x\" target=\"_blank\" rel=\"noopener\">Hughes et al., 2019<\/a>, PMID: 30464214)<\/li>\n<li>Fe-IMAC enrichment of phosphorylated peptides (<a href=\"https:\/\/doi.org\/10.15252\/msb.20199021\" target=\"_blank\" rel=\"noopener\">Leutert et al., 2019<\/a>, PMID: 31885202)<\/li>\n<\/ul>\n<\/article>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d3ac702e-be98-40ef-a5d0-8f197130092d\"><h2 class=\"vf-u-sr-only\">Liquid Chromatography<\/h2>\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"225\" height=\"300\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Agilent1200-225x300.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Agilent1200-225x300.jpg 225w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Agilent1200-768x1024.jpg 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Agilent1200-1152x1536.jpg 1152w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Agilent1200-1536x2048.jpg 1536w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Agilent1200.jpg 1617w\" sizes=\"auto, (max-width: 225px) 100vw, 225px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Agilent 1260 Infinity HPLC\n    <\/h3>\n\n  <ul>\n<li>Offline fractionation of peptides by high pH reverse phase chromatography<\/li>\n<li>Offline fractionation of crosslinked peptides by peptide size-exclusion chromatography<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"300\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Dionex-300x300.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Dionex-300x300.jpg 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Dionex-150x150.jpg 150w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Dionex.jpg 650w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Ultimate 3000 HPLC\n    <\/h3>\n\n  <ul>\n<li>Offline fractionation of peptides<\/li>\n<li>Online C18 reverse phase chromatography directly coupled to the mass spectrometer<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"300\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/vanquish-neo-uhplc-front-view-2500x2500-1-300x300.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/vanquish-neo-uhplc-front-view-2500x2500-1-300x300.jpg 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/vanquish-neo-uhplc-front-view-2500x2500-1-150x150.jpg 150w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/vanquish-neo-uhplc-front-view-2500x2500-1.jpg 650w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Vanquish Neo HPLC\n    <\/h3>\n\n  <ul>\n<li>Online fractionation of peptides with C18 reverse phase chromatography directly coupled to the mass spectrometer<\/li>\n<\/ul>\n<\/article>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-5c164ca2-1984-4606-b311-8580756f05f7\"><h2 class=\"vf-u-sr-only\">Mass Spectrometry<\/h2>\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"279\" height=\"300\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Q-Exactive-Plus-Front.avif\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Q Exactive Plus\n    <\/h3>\n\n  <p class=\"vf-summary__text\">High-resolution mass spectrometer<\/p>\n<ul>\n<li>Equipped with advanced quadrupole technology and high-resolution Orbitrap<\/li>\n<li>Fragmentation of precursor ions using HCD<\/li>\n<li>For analyses of peptides in DDA and DIA mode<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"206\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Orbitrap-Fusion-Lumos-Tribrid-Mass-Spectrometer-1-300x206.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Orbitrap-Fusion-Lumos-Tribrid-Mass-Spectrometer-1-300x206.jpg 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/Orbitrap-Fusion-Lumos-Tribrid-Mass-Spectrometer-1.jpg 482w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Orbitrap Lumos Tribrid\n    <\/h3>\n\n  <p class=\"vf-summary__text\">High-resolution mass spectrometer<\/p>\n<ul>\n<li>Equipped with advanced quadrupole technology, a high-resolution Orbitrap and synchronous precursor selection (SPS)-able Iontrap for MS3-based methods<\/li>\n<li>Fragmentation of precursor ions using HCD, CID or ETD<\/li>\n<li>For analyses of peptides in DDA and DIA mode including MS3-based methods and ETD fragmentation for PTM analysis<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"300\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/orbitrap-exploris-480-optamax-2000x2000-1.avif\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Orbitrap Exploris 480\n    <\/h3>\n\n  <p class=\"vf-summary__text\">High-resolution mass spectrometer<\/p>\n<ul>\n<li>Equipped with advanced quadrupole technology and high-resolution Orbitrap<\/li>\n<li>Fragmentation of precursor ions with HCD<\/li>\n<li>For analyses of peptides in DDA and DIA mode, especially well suited for DIA due to faster transit times<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"300\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/olympus-mass-spectrometer-facing-left-3000x3000-1-300x300.webp\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/olympus-mass-spectrometer-facing-left-3000x3000-1-300x300.webp 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/olympus-mass-spectrometer-facing-left-3000x3000-1-150x150.webp 150w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/olympus-mass-spectrometer-facing-left-3000x3000-1.webp 650w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Orbitrap Astral\n    <\/h3>\n\n  <p class=\"vf-summary__text\">Next-generation, high resolution mass spectrometer<\/p>\n<ul>\n<li>Equipped with advanced quadrupole technology, high-resolution Orbitrap and the new, sensitive, fast and high-resolution Astral analyser<\/li>\n<li>Fragmentation of precursor ions with HCD<\/li>\n<li>For ultra-deep, sensitive analyses of peptides in DDA and especially DIA mode<\/li>\n<\/ul>\n<\/article>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-939ed7f8-9c65-48c4-8251-6e773e4ea515\"><h2 class=\"vf-u-sr-only\">Data Analysis<\/h2>\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"233\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dda_analysis_v2-300x233.png\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dda_analysis_v2-300x233.png 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dda_analysis_v2-1024x794.png 1024w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dda_analysis_v2-768x596.png 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dda_analysis_v2-1536x1191.png 1536w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dda_analysis_v2-2048x1588.png 2048w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    DDA data\n    <\/h3>\n\n  <ul>\n<li>MSFragger\/FragPipe<\/li>\n<li>MaxQuant<\/li>\n<li>Skyline<\/li>\n<li>R for statistical analysis and data visualization<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"225\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dia_analysis-300x225.png\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dia_analysis-300x225.png 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dia_analysis-1024x768.png 1024w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dia_analysis-768x576.png 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dia_analysis-1536x1152.png 1536w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/dia_analysis-2048x1536.png 2048w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    DIA data\n    <\/h3>\n\n  <ul>\n<li>DIA-NN<\/li>\n<li>Skyline<\/li>\n<li>R for statistical analysis and data visualization<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"217\" src=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/XL_analysis-300x217.png\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/XL_analysis-300x217.png 300w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/XL_analysis-1024x742.png 1024w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/XL_analysis-768x557.png 768w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/XL_analysis-1536x1113.png 1536w, https:\/\/www.embl.org\/groups\/proteomics\/wp-content\/uploads\/2025\/09\/XL_analysis-2048x1484.png 2048w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Crosslinking data\n    <\/h3>\n\n  <ul>\n<li>pLink3<\/li>\n<li>xiView<\/li>\n<\/ul>\n<\/article>\n\n\n\n<hr class=\"vf-divider\">\n<\/section>\n<\/div><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n<div class=\"vf-links\">\n      <h3 class=\"vf-links__heading\">For more information, please check the vendor&#8217;s pages<\/h3>\n    <ul class=\"vf-links__list vf-list\">\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.thermofisher.com\/de\/en\/home\/life-science\/dna-rna-purification-analysis\/automated-purification-extraction\/kingfisher-systems\/models\/kingfisher-apex.html\">\n        KingFisher Apex      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.thermofisher.com\/de\/de\/home\/industrial\/chromatography\/liquid-chromatography-lc\/hplc-uhplc-systems\/ultimate-3000-hplc-uhplc-systems.html\">\n        Ultimate 3000      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/de\/en\/VN-S10-A-01\">\n        Vanquish Neo      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/IQLAAEGAAPFALGMBDK\">\n        QExactive Plus      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/IQLAAEGAAPFADBMBHQ\">\n        Orbitrap Tribrid Lumos      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.thermofisher.com\/de\/en\/home\/industrial\/mass-spectrometry\/liquid-chromatography-mass-spectrometry-lc-ms\/lc-ms-systems\/orbitrap-lc-ms\/orbitrap-exploris-mass-spectrometers\/orbitrap-exploris-480-mass-spectrometers.html\">\n        Orbitrap Exploris 480      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"http:\/\/thermofisher.com\/de\/de\/home\/industrial\/mass-spectrometry\/liquid-chromatography-mass-spectrometry-lc-ms\/lc-ms-systems\/orbitrap-lc-ms\/orbitrap-astral-mass-spectrometer.html\">\n        Orbitrap Astral      <\/a>\n      <\/li>\n  <\/ul>\n\n<\/div>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":15,"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-24119","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/pages\/24119","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\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/comments?post=24119"}],"version-history":[{"count":45,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/pages\/24119\/revisions"}],"predecessor-version":[{"id":24757,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/pages\/24119\/revisions\/24757"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/media?parent=24119"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/proteomics\/wp-json\/wp\/v2\/embl_taxonomy?post=24119"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}