{"id":2859,"date":"2024-07-24T15:56:46","date_gmt":"2024-07-24T19:56:46","guid":{"rendered":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/?page_id=2859"},"modified":"2025-07-03T13:46:21","modified_gmt":"2025-07-03T17:46:21","slug":"proteomics-services","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/services-and-rates\/proteomics-services\/","title":{"rendered":"Proteomics Services"},"content":{"rendered":"<som-cell cell-info=\"{&quot;ID&quot;:3011,&quot;post_author&quot;:&quot;112631&quot;,&quot;post_date&quot;:&quot;2024-08-09 10:37:11&quot;,&quot;post_date_gmt&quot;:&quot;2024-08-09 14:37:11&quot;,&quot;post_content&quot;:&quot;&quot;,&quot;post_title&quot;:&quot;Proteomics Services \\u2013 Content Boxes&quot;,&quot;post_excerpt&quot;:&quot;&quot;,&quot;post_status&quot;:&quot;publish&quot;,&quot;comment_status&quot;:&quot;closed&quot;,&quot;ping_status&quot;:&quot;closed&quot;,&quot;post_password&quot;:&quot;&quot;,&quot;post_name&quot;:&quot;services-content-boxes&quot;,&quot;to_ping&quot;:&quot;&quot;,&quot;pinged&quot;:&quot;&quot;,&quot;post_modified&quot;:&quot;2025-07-03 15:46:03&quot;,&quot;post_modified_gmt&quot;:&quot;2025-07-03 19:46:03&quot;,&quot;post_content_filtered&quot;:&quot;&quot;,&quot;post_parent&quot;:0,&quot;guid&quot;:&quot;https:\\\/\\\/www.med.unc.edu\\\/proteomics-metabolomics\\\/cell\\\/services-content-boxes\\\/&quot;,&quot;menu_order&quot;:0,&quot;post_type&quot;:&quot;somcell&quot;,&quot;post_mime_type&quot;:&quot;&quot;,&quot;comment_count&quot;:&quot;0&quot;,&quot;filter&quot;:&quot;raw&quot;}\" cell-meta=\"{&quot;_wpv_contains_gutenberg_views&quot;:[&quot;&quot;],&quot;_upd_sortorder&quot;:[&quot;1&quot;],&quot;layout&quot;:[&quot;RepeatableBoxes&quot;],&quot;cellInformation&quot;:[&quot;{\\&quot;singleCellBlocks\\&quot;:{},\\&quot;repeatableBoxes\\&quot;:[{\\&quot;boxText\\&quot;:\\&quot;Global Proteomic Profiling\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;Identification and quantification of proteins in a complex mixture, which can be submitted either in-gel or in-solution. Depending on sample complexity, hundreds to thousands of proteins can be detected in a single analysis. In some cases, &gt; 10,000 proteins can be identified. \\\\nQuantitation allows measurement of the relative changes in protein abundances between controls and samples to identify significantly regulated proteins. We routinely use (and prefer) data-independent (DIA) label-free quantitation (LFQ), especially for large sample sizes and\\\/or clinical samples. If label-based quantitation is preferred, we use Tandem Mass Tags (TMT; Thermo Scientific) and we can multiplex up to 18 samples. \\\\n\\\\n\\\\nPlasma proteomics\\\\n\\\\nWe offer multiple options for proteomic analysis of plasma or serum from human, mouse, and other species. From neat human plasma, we routinely identify up to 1,000 proteins. For deeper profiling, the Seer Proteograph ONE Workflow enables the identification of up to 7,000 proteins from human plasma. Additional sample preparation strategies\\u2014such as acid depletion or extracellular vesicle enrichment\\u2014are also available. Please contact our staff to discuss the best approach for your project and for pricing information.\\\\n\\\\n\\\\nMetaproteomics\\\\n\\\\nWe offer metaproteomics analysis for microbiome studies. Please note that a suitable protein sequence database will need to be provided, which can be either a reference database or one derived from a matched metagenome. \\&quot;,\\&quot;useRichTextEditor\\&quot;:\\&quot;true\\&quot;,\\&quot;boxRichText\\&quot;:\\&quot;&lt;p&gt;Identification and quantification of proteins in a complex mixture, which can be submitted either in-gel or in-solution. Depending on sample complexity, hundreds to thousands of proteins can be detected in a single analysis. In some cases, &gt; 10,000 proteins can be identified.&nbsp;&lt;\\\/p&gt;&lt;p&gt;Quantitation allows measurement of the relative changes in protein abundances between controls and samples to identify significantly regulated proteins. We routinely use (and prefer) data-independent (DIA) label-free quantitation (LFQ), especially for large sample sizes and\\\/or clinical samples. If label-based quantitation is preferred, we use Tandem Mass Tags (TMT; Thermo Scientific) and we can multiplex up to 18 samples.&nbsp;&lt;\\\/p&gt;&lt;p&gt;&lt;strong&gt;Plasma proteomics&lt;\\\/strong&gt;&lt;\\\/p&gt;&lt;p&gt;We offer multiple options for proteomic analysis of plasma or serum from human, mouse, and other species. From neat human plasma, we routinely identify up to 1,000 proteins. For deeper profiling, the Seer Proteograph ONE Workflow enables the identification of up to 7,000 proteins from human plasma. Additional sample preparation strategies\\u2014such as acid depletion or extracellular vesicle enrichment\\u2014are also available. Please contact our staff to discuss the best approach for your project and for pricing information.&lt;\\\/p&gt;&lt;p&gt;&lt;strong&gt;Metaproteomics&lt;\\\/strong&gt;&lt;\\\/p&gt;&lt;p&gt;We offer metaproteomics analysis for microbiome studies. Please note that a suitable protein sequence database will need to be provided, which can be either a reference database or one derived from a matched metagenome.&nbsp;&lt;\\\/p&gt;\\&quot;},{\\&quot;includeLink\\&quot;:1,\\&quot;boxText\\&quot;:\\&quot;Affinity Purification-Mass Spectrometry (AP-MS) Analysis\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;Identification of protein binding partners of proteins captured using affinity purification including traditional immunoprecipitation approaches (endogenous or overexpressed\\\/tagged proteins) and proximity labeling-based approaches (BioID, APEX, TurboID, etc). AP-MS also includes other types of pulldowns such as DNA, RNA, lectin pulldowns to identify protein interactors of these molecules. There are critical sample preparation steps that must be considered before submitting these types of samples, so please contact the staff to discuss the project prior to sample preparation. Each sample MUST be submitted with a proper control.\\&quot;,\\&quot;useRichTextEditor\\&quot;:\\&quot;true\\&quot;,\\&quot;boxRichText\\&quot;:\\&quot;&lt;p&gt;We offer identification of protein binding partners using affinity purification approaches, including traditional immunoprecipitation (for endogenous or overexpressed\\\/tagged proteins) as well as proximity labeling methods such as BioID, APEX, and TurboID.&lt;\\\/p&gt;&lt;p&gt;AP-MS also supports other types of pulldown experiments\\u2014including DNA, RNA, and lectin pulldowns\\u2014to identify protein interactors of these molecules.&lt;\\\/p&gt;&lt;p&gt;Please note: there are critical sample preparation steps that must be planned in advance. We strongly recommend contacting our staff to discuss your project before preparing samples. Each sample must be submitted with an appropriate control.&lt;\\\/p&gt;\\&quot;},{\\&quot;boxText\\&quot;:\\&quot;Global Post-translational Modification (PTM) Profiling\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;Global Phosphoproteomics\\\\nOur most common PTM profiling service is global quantitative phosphoproteomics. A typical global phosphoproteomics workflow involves TMT-based quantitation, offline HPLC fractionation, and High Select FeNTA enrichment. Depending on sample complexity, hundreds to thousands of phosphopeptides can be detected in a single analysis. In some cases, &gt; 20,000 phospho sites can be detected.\\\\n\\\\nAdditional PTMs such as ubiquitylation, acetylation, and methylation (using Cell Signaling Technology\\u2019s antibody-based kits) can also be profiled on a global level.\\&quot;,\\&quot;useRichTextEditor\\&quot;:\\&quot;true\\&quot;,\\&quot;boxRichText\\&quot;:\\&quot;&lt;p&gt;&lt;strong&gt;Global Phosphoproteomics&lt;\\\/strong&gt;&lt;\\\/p&gt;&lt;p&gt;Our most common PTM profiling service is global quantitative phosphoproteomics. A typical global phosphoproteomics workflow involves TMT-based quantitation, offline HPLC fractionation, and High Select FeNTA enrichment. Depending on sample complexity, hundreds to thousands of phosphopeptides can be detected in a single analysis. In some cases, &gt; 20,000 phospho sites can be detected.&lt;\\\/p&gt;&lt;p&gt;&lt;strong&gt;PTM Peptide-Based IPs&lt;\\\/strong&gt;&lt;\\\/p&gt;&lt;p&gt;Additional PTMs such as ubiquitylation, acetylation, and methylation (using Cell Signaling Technology\\u2019s antibody-based kits) can also be profiled on a global level.&lt;\\\/p&gt;\\&quot;},{\\&quot;boxText\\&quot;:\\&quot;Post-translational Modification (PTM) Site Mapping\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;\\&quot;,\\&quot;useRichTextEditor\\&quot;:\\&quot;true\\&quot;,\\&quot;boxRichText\\&quot;:\\&quot;&lt;p&gt;We offer analysis of highly purified proteins to identify and localize post-translational modifications (PTMs), using either in-gel or in-solution samples. Common PTMs include phosphorylation, ubiquitination, acetylation, and methylation. If you&#039;re interested in detecting a specific modification, please contact us - our team can recommend optimized sample preparation protocols tailored to your target PTM.&lt;\\\/p&gt;&lt;p&gt;To confirm PTMs at specific residues, the MAP Core staff be able to apply targeted mass spectrometry approaches to specifically detect the modified peptide of interest. Reach out to discuss whether a targeted strategy is appropriate for your project.&lt;\\\/p&gt;\\&quot;},{\\&quot;boxText\\&quot;:\\&quot;Protein Identification from a gel band\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;A highly purified protein, visible by Coomassie, is submitted in-gel; most abundant protein(s) can be detected.\\&quot;},{\\&quot;boxText\\&quot;:\\&quot;Protein Characterization\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;\\&quot;,\\&quot;useRichTextEditor\\&quot;:\\&quot;true\\&quot;,\\&quot;boxRichText\\&quot;:\\&quot;&lt;p&gt;Expanding on our Protein ID service, this offering provides more detailed analysis of a single, highly purified protein (in-solution or in-gel). For example -&nbsp;determining protein purity, confirming a mutated amino acid (location-dependent), or confirming protein truncation (sequence-dependent).&lt;\\\/p&gt;&lt;p&gt;&lt;br&gt;&lt;\\\/p&gt;\\&quot;},{\\&quot;boxExcerptText\\&quot;:\\&quot;\\\\n\\\\nMultiplex Inhibitor Bead Coupled to Mass Spectrometry (MIB-MS) Kinome Profiling\\\\n\\\\nThermal Proteome Profiling (TPP)\\\\nThermal Proteome Profiling (TPP) is a mass spectrometry\\u2013based technique that measures changes in protein thermal stability across conditions to identify drug targets and study protein\\u2013ligand interactions in complex samples. It enables proteome-wide assessment of binding events and stability shifts in living cells or lysates.\\&quot;,\\&quot;boxText\\&quot;:\\&quot;Chemoproteomics\\&quot;,\\&quot;useRichTextEditor\\&quot;:\\&quot;true\\&quot;,\\&quot;boxRichText\\&quot;:\\&quot;&lt;p&gt;Chemoproteomics services include identification of protein targets and off-targets from drug-protein pulldown experiments or activity-based protein profiling (ABPP). Customers are expected to provide samples post-pulldown; however, MAP Core staff offer comprehensive consultation to support experimental design and optimization.&lt;\\\/p&gt;&lt;p&gt;We also specialize in the identification and site-specific localization of covalent modifications, such as drug adducts or reactive compound binding, on highly purified proteins. For accurate detection, customers must provide the exact mass of the compound. When appropriate, an open search strategy can be applied to detect unexpected or novel modifications.&lt;\\\/p&gt;&lt;p&gt;We also offer full-service chemoproteomics services such as:&lt;\\\/p&gt;&lt;p&gt;&lt;strong&gt;Multiplex Inhibitor Bead Coupled to Mass Spectrometry (MIB-MS)&lt;\\\/strong&gt;&lt;\\\/p&gt;&lt;p&gt;This service is performed in collaboration with Dr. Lee Graves\\u2019 lab, please contact him with inquiries. Immobilized pan kinase inhibitors are used to capture kinases from a complex sample. Depending on sample type, up to 400 kinases can be enriched, which are subsequently digested with trypsin and analyzed by LC-MS\\\/MS. Relative quantitation of kinases is performed to identify kinome changes between samples. Biological replicates are required.&lt;\\\/p&gt;&lt;p&gt;&lt;strong&gt;Thermal Proteome Profiling (TPP)&lt;\\\/strong&gt;&lt;\\\/p&gt;&lt;p&gt;This technique measures changes in protein thermal stability across conditions to identify drug targets and study protein\\u2013ligand interactions in complex samples. It enables proteome-wide assessment of binding events and stability shifts in living cells or lysates. Reach out to discuss whether TPP is appropriate for your project.&lt;\\\/p&gt;&lt;p&gt;&lt;br&gt;&lt;\\\/p&gt;\\&quot;},{\\&quot;boxText\\&quot;:\\&quot;Targeted Proteomics Analysis\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;We offer targeted LC-MS\\\/MS analysis to confirm and\\\/or quantify specific proteins or peptides of interest within complex samples. For this, parallel reaction monitoring (PRM) acquisition mode is commonly used on our mass spectrometers.  When applicable, synthetic peptides can be used to enhance detection or enable absolute quantitation. These peptides must be supplied by the customer.\\&quot;},{\\&quot;boxText\\&quot;:\\&quot;High-resolution Intact Mass Analysis for peptides\\\/proteins (Proteomics)\\&quot;,\\&quot;boxExcerptText\\&quot;:\\&quot;This analysis is typically performed using the 908 Devices CE ZipChip coupled to the Thermo Q Exactive HF. Proteins or peptides can be submitted either lyophilized or in solution; please contact us for specific buffer and concentration requirements.\\\\nIntact molecular weights are determined with high mass accuracy (at the ppm level) using one of our high-resolution Orbitrap instruments. This service is ideal when precise mass measurement is needed, such as for confirming post-translational modifications (PTMs) or other molecular changes.\\&quot;,\\&quot;useRichTextEditor\\&quot;:\\&quot;true\\&quot;,\\&quot;boxRichText\\&quot;:\\&quot;&lt;p&gt;We offer high-resolution intact mass analysis for proteins and peptides using the 908 Devices ZipChip capillary electrophoresis (CE) system coupled to an Orbitrap mass spectrometer. This platform enables rapid, high-sensitivity analysis with exceptional mass accuracy. Samples may be submitted either lyophilized or in solution. Please contact MAP Core staff in advance for guidance on buffer compatibility and concentration requirements.&lt;\\\/p&gt;&lt;p&gt;Mass spectra are acquired with ppm-level accuracy and analyzed using specialized software to deconvolute m\\\/z values and determine intact molecular masses. This service is ideal for confirming molecular identity, detecting post-translational modifications (PTMs), or verifying other precise molecular changes.&lt;\\\/p&gt;\\&quot;}],\\&quot;boxCustomStyles\\&quot;:{\\&quot;textAlign\\&quot;:\\&quot;left\\&quot;,\\&quot;includeImage\\&quot;:0,\\&quot;includeImagePadding\\&quot;:1,\\&quot;imageAspectRatio\\&quot;:\\&quot;3\\\/2\\&quot;,\\&quot;includeLink\\&quot;:0,\\&quot;backgroundColor\\&quot;:\\&quot;lightBlue\\&quot;,\\&quot;columnLayout\\&quot;:\\&quot;2\\&quot;},\\&quot;boxType\\&quot;:\\&quot;imageBoxes\\&quot;,\\&quot;boxStyleOption\\&quot;:\\&quot;content-boxes\\&quot;}&quot;],&quot;apiCallInformation&quot;:[&quot;{}&quot;]}\"><\/som-cell>\n<div class=\"bs-callout bs-callout-primary\">\n<h3>*Quantitation<\/h3>\n<p>The analyses described above are quantitative. Quantitation of peptides\/proteins is typically performed to compare a sample to a control (e.g. post-drug treatment, post-knockdown, etc.). Please contact the MAP Core staff to discuss experimental design.<\/p>\n<p><strong>Types of quantitation include:<\/strong><\/p>\n<ol>\n<li>Isobaric tagging (TMT). The facility provides the labels and will perform the labeling step \u2013 up to 18 samples can be multiplexed.<\/li>\n<li>Label-free Data Dependent Acquisition (DDA) using area under the curve or spectral counting. Each sample is analyzed individually. No additional sample preparation required.<\/li>\n<li>Label-free Data Independent Acquisition (DIA) using peak areas in a library-based or Direct-DIA approach. Each sample is analyzed individually. No additional sample preparation required.<\/li>\n<li><em>Absolute quantitation using heavy labeled peptides for targeted analysis of specific peptides\/proteins *only for targeted analyses (see above).<\/em><\/li>\n<\/ol>\n<p>Proteins are typically digested with trypsin then analyzed by LC-MS\/MS. Peptide\/proteins are identified and quantified using Spectronaut (Label-free DIA), Proteome Discoverer (TMT, label-free DDA), MaxQuant (label-free DDA, <em>APMS projects only<\/em>), or FragPipe (label-free DDA). Further data analysis is conducted in Perseus, and\/or R. The MAP Core can provide publication quality figures such as bar graphs, volcano plots, PCA plots, hierarchical clustering with heat maps, pathway enrichment plots, as well as perform bioinformatics analyses using DAVID or IPA, among other programs.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>*Quantitation The analyses described above are quantitative. Quantitation of peptides\/proteins is typically performed to compare a sample to a control (e.g. post-drug treatment, post-knockdown, etc.). Please contact the MAP Core staff to discuss experimental design. Types of quantitation include: Isobaric tagging (TMT). The facility provides the labels and will perform the labeling step \u2013 up &hellip; <a href=\"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/services-and-rates\/proteomics-services\/\" aria-label=\"Read more about Proteomics Services\">Read more<\/a><\/p>\n","protected":false},"author":112631,"featured_media":0,"parent":2258,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2859","page","type-page","status-publish","hentry","odd"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Proteomics Services - Michael Hooker Metabolomics and Proteomics Core<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/services-and-rates\/proteomics-services\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Proteomics Services - Michael Hooker Metabolomics and Proteomics Core\" \/>\n<meta property=\"og:description\" content=\"*Quantitation The analyses described above are quantitative. 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