{"id":66514,"date":"2024-05-14T13:54:19","date_gmt":"2024-05-14T17:54:19","guid":{"rendered":"https:\/\/www.crchudequebec.ulaval.ca\/platforms-and-services\/genomics-center\/proteomique\/proteomique-quantitative\/"},"modified":"2024-07-05T11:54:31","modified_gmt":"2024-07-05T15:54:31","slug":"proteomique-quantitative","status":"publish","type":"page","link":"https:\/\/www.crchudequebec.ulaval.ca\/en\/platforms-and-services\/genomics-center\/proteomique\/proteomique-quantitative\/","title":{"rendered":"Quantitative Proteomics"},"content":{"rendered":"<section class=\"bg-white align wp-block-acf-content-with-left-sidebar\">\n    <div class=\"container\">\n    <div class=\"padd padd--bottom\">\n        <div class=\"wrap\">\n            <div class=\"flex md:flex-row flex-col md:gap-x-[8.3%] gap-x-3 md:gap-y-0 gap-y-8\">\n                <div class=\"sidebar md:w-1\/4 w-full flex flex-col gap-y-8\">\n                    \n                    \n                                                                        <div>\n                                                                    <h3 class=\"mb-0 text-16 font-bold\">Director<\/h3>\n                                \n                                                                    <div class=\"mb-1\">\n                                        Arnaud Droit, Ph.D.\n                                    <\/div>\n                                \n                                \n                                \n                                                            <\/div>\n                                                    <div>\n                                                                    <h3 class=\"mb-0 text-16 font-bold\">Coordinator<\/h3>\n                                \n                                                                    <div class=\"mb-1\">\n                                        Florence Roux-Dalvai, M.Sc.\n                                    <\/div>\n                                \n                                \n                                \n                                                            <\/div>\n                                                    <div>\n                                                                    <h3 class=\"mb-0 text-16 font-bold\">Proteomics<\/h3>\n                                \n                                                                    <div class=\"mb-1\">\n                                        2705 boul. Laurier, local R2-2710<br \/>\r\nQu\u00e9bec (Qu\u00e9bec) Canada G1V 4G2\n                                    <\/div>\n                                \n                                                                    <div class=\"mb-1\">\n                                                                                    \n                                            <a class=\"phone\" href=\"tel:+1 418-654-2261\">+1 418-654-2261<\/a>\n                                                                                    \n                                            <a class=\"phone\" href=\"tel:+1 418-654-2159 (fax)\">+1 418-654-2159 (fax)<\/a>\n                                                                            <\/div>\n                                \n                                                                    <ul class=\"emails !mb-3\">\n                                                                                    <li class=\"overflow-hidden\">\n                                                <a class=\"group flex items-center\" href=\"mailto:prot\u00e9omique@crchudequebec.ulaval.ca\" title=\"prot\u00e9omique@crchudequebec.ulaval.ca\">\n                                                    <i class=\"fa-light fa-envelope shrink-0 group-hover:text-blue-500 duration-300\"><\/i>\n                                                    <span class=\"text-16 whitespace-nowrap overflow-hidden text-ellipsis group-hover:text-blue-500 duration-300\">prot\u00e9omique@crchudequebec.ulaval.ca<\/span>\n                                                <\/a>\n                                            <\/li>\n                                                                            <\/ul>\n                                \n                                                            <\/div>\n                                            \n                    \n                    \n                    \n                                    <\/div>\n                <div class=\"main-content md:w-7\/12 w-full\">\n                    \n                    \n                                            <div class=\"content\">\n                            <div class=\"inner\">\n                                <p><span class=\"TextRun SCXW207030922 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW207030922 BCX0\">In addition to <\/span><\/span><a href=\"https:\/\/www.crchudequebec.ulaval.ca\/en\/platforms-and-services\/genomics-center\/proteomique\/identification-des-proteines\/\" target=\"_blank\" rel=\"noopener\"><span class=\"TextRun Highlight SCXW207030922 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW207030922 BCX0\">protein<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> identification<\/span><\/span><\/a><span class=\"TextRun SCXW207030922 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW207030922 BCX0\">, <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">it<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">is<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> possible to <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">obtain<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> quantification data <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">from<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> LC-MS\/MS <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">proteomic<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> analyses. <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">Except<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> in <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">sp<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">ecial<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> cases<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> of <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">targeted<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">proteomics<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">, the quantification <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">obtained<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">is<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">always<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> relative. That <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">is<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">, for <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">each<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">protein<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">, <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">we<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">obtain<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> a ratio <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">between<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">different<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\"> groups<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">\/conditions to <\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">be<\/span> <span class=\"NormalTextRun SCXW207030922 BCX0\">compared<\/span><span class=\"NormalTextRun SCXW207030922 BCX0\">.<\/span><\/span><span class=\"EOP SCXW207030922 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span class=\"TextRun SCXW120168671 BCX0\" lang=\"FR-FR\" xml:lang=\"FR-FR\" data-contrast=\"none\"><span class=\"NormalTextRun SpellingErrorV2Themed SCXW120168671 BCX0\">Two<\/span><span class=\"NormalTextRun SCXW120168671 BCX0\"> quantification <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW120168671 BCX0\">methods<\/span><span class=\"NormalTextRun SCXW120168671 BCX0\"> are <\/span><span class=\"NormalTextRun SCXW120168671 BCX0\">possible<\/span> <span class=\"NormalTextRun SCXW120168671 BCX0\">:<\/span><\/span><span class=\"EOP SCXW120168671 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h4><span class=\"TextRun SCXW10180488 BCX0\" lang=\"FR-FR\" xml:lang=\"FR-FR\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW10180488 BCX0\">Chemical <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW10180488 BCX0\">labeling<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW10180488 BCX0\">with<\/span><span class=\"NormalTextRun SCXW10180488 BCX0\"> TMT (Tandem Mass Tag)<\/span><\/span><span class=\"EOP SCXW10180488 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h4>\n<p><span class=\"TextRun SCXW99158606 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW99158606 BCX0\">With<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">this<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">method<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">, peptides <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">from<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">each<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">sample<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> are <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">labeled<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">with<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> a <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">chemical<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> compound <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">tagged<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">with<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> stable isotopes. <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">Each<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">sample<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">receives<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> a <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">different<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> label, and <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">then<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> the <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">samples<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> are <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">combined<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> and <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">injected<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">together<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">into<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> the mass <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">spectrometer<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">, <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">which<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">generates<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> MS1 and MS2 <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">spectra<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> as in <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">a<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> simple identification <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">analysis<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">. <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">However<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">, <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">during<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> fragmentation, the <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">different<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> tags <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">generate<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> reporter ions (one for <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">each<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">sample<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">). <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">Thus<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">, the MS2 <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">spectra<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">contain<\/span> <span class=\"NormalTextRun ContextualSpellingAndGrammarErrorV2Themed SCXW99158606 BCX0\">the fragments<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> for <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">identifying<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> the peptide <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">it<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">contains<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> as <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">well<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> as <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">a<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> group of reporter ions <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">whose<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">intensities<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">provide<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> the quantification of <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">this<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\"> peptide in <\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">each<\/span> <span class=\"NormalTextRun SCXW99158606 BCX0\">sample<\/span><span class=\"NormalTextRun SCXW99158606 BCX0\">.<\/span><\/span><span class=\"EOP SCXW99158606 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-65196\" src=\"https:\/\/www.crchudequebec.ulaval.ca\/wp-content\/uploads\/2024\/06\/Proteomique_Services_ProteomiqueQuantitative-e1718800713185.png\" alt=\"\" width=\"800\" height=\"371\" \/><\/p>\n<p><span class=\"TextRun SCXW103416393 BCX0\" lang=\"FR-FR\" xml:lang=\"FR-FR\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW103416393 BCX0\">This <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW103416393 BCX0\">method<\/span><span class=\"NormalTextRun SCXW103416393 BCX0\"> can <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW103416393 BCX0\">be<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW103416393 BCX0\">used<\/span><span class=\"NormalTextRun SCXW103416393 BCX0\"> in <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW103416393 BCX0\">two<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW103416393 BCX0\">different<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW103416393 BCX0\">contexts<\/span><span class=\"NormalTextRun SCXW103416393 BCX0\">:<\/span><\/span><span class=\"EOP SCXW103416393 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<ul>\n<li><span class=\"TextRun SCXW134327772 BCX0\" lang=\"FR-FR\" xml:lang=\"FR-FR\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW134327772 BCX0\">For <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">experiments<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">with<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> 18 <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">samples<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> or <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">less<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\">: TMT <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">labeling<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> can <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">be<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">used<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> to combine <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">samples<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> and <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">then<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">fractionate<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">them<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> (<\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">usually<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> 12 fractions <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">obtained<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\"> by high pH <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">fractionation<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\">) to <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">obtain<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">better<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">proteome<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW134327772 BCX0\">coverage<\/span><span class=\"NormalTextRun SCXW134327772 BCX0\">.<\/span><\/span><span class=\"EOP SCXW134327772 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/li>\n<li><span class=\"TextRun SCXW63622681 BCX0\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW63622681 BCX0\">On the <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">contrary<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">, for <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">experiments<\/span> <span class=\"NormalTextRun SCXW63622681 BCX0\">with<\/span> <span class=\"NormalTextRun SCXW63622681 BCX0\">a <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">very<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\"> large<\/span> <span class=\"NormalTextRun SCXW63622681 BCX0\">number<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\"> of <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">samples<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">, TMT <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">labeling<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\"> can <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">be<\/span> <span class=\"NormalTextRun SCXW63622681 BCX0\">used<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\"> to multiplex the analyses (up to 17 <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">samples<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\"> + 1 <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">normalization<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\"> control in the <\/span><span class=\"NormalTextRun SCXW63622681 BCX0\">same<\/span><span class=\"NormalTextRun SCXW63622681 BCX0\"> injection).<\/span><\/span><span class=\"EOP SCXW63622681 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/li>\n<\/ul>\n<p><span class=\"TextRun SCXW84719077 BCX0\" lang=\"FR-FR\" xml:lang=\"FR-FR\" data-contrast=\"none\"><span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">However<\/span><span class=\"NormalTextRun SCXW84719077 BCX0\">, <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">this<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">method<\/span><span class=\"NormalTextRun SCXW84719077 BCX0\"> has <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">two<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">disadvantages<\/span><span class=\"NormalTextRun SCXW84719077 BCX0\">: <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">it<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">is<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">quite<\/span> <span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">expensive<\/span><span class=\"NormalTextRun SCXW84719077 BCX0\"> (TMT <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">labeling<\/span><span class=\"NormalTextRun SCXW84719077 BCX0\"> kit), and <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">it<\/span><span class=\"NormalTextRun SCXW84719077 BCX0\"> can <\/span><span class=\"NormalTextRun SpellingErrorV2Themed SCXW84719077 BCX0\">generate<\/span><span class=\"NormalTextRun SCXW84719077 BCX0\"> ratio compression.<\/span><\/span><span class=\"EOP SCXW84719077 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h4><span class=\"TextRun SCXW142668591 BCX0\" lang=\"FR-FR\" xml:lang=\"FR-FR\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW142668591 BCX0\">Label-Free Quantification (LFQ)<\/span><\/span><span class=\"EOP SCXW142668591 BCX0\" data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h4>\n<p><span data-contrast=\"none\">This is the simplest method. Samples are treated separately and injected one after the other into the mass spectrometer.<\/span><span data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">Depending on the experiments and instruments, we use two different signal acquisition strategies called DDA (Data Dependent Acquisition) or DIA (Data Independent Acquisition). DDA acquisition provides higher-quality spectra (necessary, for example, for the analysis of post-translational modifications), while DIA analysis generally allows for more comprehensive proteome coverage.<\/span><span data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">After analysis, signal processing software allows us to obtain quantification values by reconstituting and integrating the peak area of each peptide elution in each sample.<\/span><span data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">This method has the advantage of being less expensive than the labeling method, and it also allows for the handling of experiments containing hundreds of samples. Bioinformatic processing methods then allow for data normalization between different injections.<\/span><span data-ccp-props=\"{&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559739&quot;:120,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n\n                            <\/div>\n                        <\/div>\n                    \n                    \n                    \n                    \n                                    <\/div>\n            <\/div>\n        <\/div>\n    <\/div>\n<\/div>\n<\/section>\n","protected":false},"excerpt":{"rendered":"<p>The quantitative proteomics service enables both the identification and relative quantification of proteins in each sample. <\/p>\n","protected":false},"author":10,"featured_media":0,"parent":46835,"menu_order":9,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-66514","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.5 - 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