{"id":2209,"date":"2026-05-03T21:09:51","date_gmt":"2026-05-03T21:09:51","guid":{"rendered":"https:\/\/research.ncsu.edu\/metric\/?page_id=2209"},"modified":"2026-11-13T12:23:54","modified_gmt":"2026-11-13T12:23:54","slug":"proteomics-protein-characterization","status":"publish","type":"page","link":"https:\/\/research.ncsu.edu\/metric\/proteomics-protein-characterization\/","title":{"rendered":"Proteomics &amp; Protein Characterization"},"content":{"rendered":"\n\n\n\n<div class=\"ncst-askew-media-text has-custombg-two-background-color wp-block-ncst-mini-story\">\n    <div class=\"ncst-askew-media-text__container\">\n      \n<div class=\"wp-block-ncst-text-column\">\n    <h2 class=\"ncst-text-column__heading\">Targeted Protein Identification<\/h2>\n    <p class=\"ncst-text-column__teaser\">Available for samples in-solution or via in-gel digestion.<\/p>\n          \n<div class=\"is-text wp-block-ncst-buttons\">\n    \n<div class=\"is-style-secondary wp-block-ncst-button\">\n      <a\n        class=\"ncst-block__button-link btn\"\n        href=\"mailto:qshu@ncsu.edu?cc=Taufika_Williams@ncsu.edu&amp;subject=Targeted%20Protein%20Identification\"\n        data-ncst-lightbox=\"false\"\n                      >\n                  <span class=\"text\">Questions?  Contact us!<\/span><span class=\"arrow-indicator\"><svg class=\"wolficon wolficon-arrow-right-bold\" role=\"img\"  aria-hidden=\"true\">\n\t\t\t\n\t\t\t<use xlink:href=\"#wolficon-arrow-right-bold\">\n\t\t<\/svg><\/span>\n              <\/a>\n    <\/div>\n  \n\n  <\/div>\n\n\n      <\/div>\n\n\n<div class=\"wp-block-ncst-media\">\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"576\" src=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/Targeted-Protein-Identification-1024x576.jpg\" alt=\"Targeted Protein Identification workflow\" class=\"wp-image-2691\" srcset=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/Targeted-Protein-Identification-1024x576.jpg 1024w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/Targeted-Protein-Identification-300x169.jpg 300w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/Targeted-Protein-Identification-768x432.jpg 768w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/Targeted-Protein-Identification.jpg 1500w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n<\/div>\n\n    <\/div>\n  <\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Description:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Identify proteins in solution or in excised gel bands using nanoLC-MS\/MS. This service can be used to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Confirm the presence of a known protein in a sample.<\/li>\n\n\n\n<li>Identify unknown proteins from organisms with available protein sequence databases.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">User provides:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Peptide samples prepared according to our <strong><a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/InSolution_Tryptic_Digest_Guanidination.pdf\">in-<\/a><a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/InSolution_Tryptic_Digest_Guanidination.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">solution<\/a><\/strong> or <strong><a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/Pierce\u2122-In-Gel-Tryptic-Digestion-Kit.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">in-gel<\/a> <\/strong>digestion protocol.<\/li>\n\n\n\n<li>The species from which the sample was derived (unknown protein identification) OR<strong> <a href=\"https:\/\/www.uniprot.org\" target=\"_blank\" rel=\"noreferrer noopener\">Uniprot ID<\/a><\/strong> (known protein).<\/li>\n\n\n\n<li>Typically, 0.05\u20132 \u00b5g of peptides is sufficient for protein identification, although the optimal amount depends on sample complexity and experimental goals.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Service performed:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Peptide samples are analyzed by nanoLC-MS\/MS on a Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer. MS\/MS spectra are searched against the appropriate protein sequence database to identify proteins and their corresponding peptides.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Report details:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Results are provided as a Proteome Discoverer report and typically include:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Identified protein(s)<\/li>\n\n\n\n<li>Peptide sequences<\/li>\n\n\n\n<li>Peptide-Spectrum Matches (PSMs)<\/li>\n\n\n\n<li>Protein sequence coverage<\/li>\n\n\n\n<li>Protein confidence metrics<\/li>\n\n\n\n<li>Identified peptide modifications (when applicable)<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/SAMPLE_in_gel_digestion_report.xlsx\" target=\"_blank\" rel=\"noreferrer noopener\">SAMPLE REPORT<\/a><\/strong><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Cost:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>$150\/sample (NC State Internal rate)<\/li>\n\n\n\n<li>$228\/sample (External academic or federally funded clients rate)<\/li>\n\n\n\n<li>$750\/sample (Commercial rate)<\/li>\n<\/ul>\n\n\n<div class=\"ncst-askew-media-text has-custombg-two-background-color mirror-layout wp-block-ncst-mini-story\">\n    <div class=\"ncst-askew-media-text__container\">\n      \n<div class=\"wp-block-ncst-text-column\">\n    <h2 class=\"ncst-text-column__heading\">Intact Protein Mass Analysis<\/h2>\n    <p class=\"ncst-text-column__teaser\">Verification of recombinant proteins, synthetic peptides, and antibodies. Ideal for confirming molecular weight, assessing purity, and identifying large-scale modifications.<\/p>\n          \n<div class=\"is-text wp-block-ncst-buttons\">\n    \n<div class=\"is-style-secondary wp-block-ncst-button\">\n      <a\n        class=\"ncst-block__button-link btn\"\n        href=\"mailto:qshu@ncsu.edu?cc=Taufika_Williams@ncsu.edu&amp;subject=Intact%20Protein%20Mass%20Analysis\"\n        data-ncst-lightbox=\"false\"\n                      >\n                  <span class=\"text\">Questions? Contact us!<\/span><span class=\"arrow-indicator\"><svg class=\"wolficon wolficon-arrow-right-bold\" role=\"img\"  aria-hidden=\"true\">\n\t\t\t\n\t\t\t<use xlink:href=\"#wolficon-arrow-right-bold\">\n\t\t<\/svg><\/span>\n              <\/a>\n    <\/div>\n  \n\n  <\/div>\n\n\n      <\/div>\n\n\n<div class=\"wp-block-ncst-media\">\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"576\" src=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/intact-mass-1024x576.jpg\" alt=\"Intact protein mass analysis\" class=\"wp-image-2692\" srcset=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/intact-mass-1024x576.jpg 1024w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/intact-mass-300x169.jpg 300w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/intact-mass-768x432.jpg 768w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/intact-mass.jpg 1500w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n<\/div>\n\n    <\/div>\n  <\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Description:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Determine the accurate molecular mass of intact proteins using high-resolution LC-MS. This service can be used to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Characterize&nbsp;glycoform distributions&nbsp;and other mass variants of antibodies and glycoproteins.<\/li>\n\n\n\n<li>Confirm the molecular weight of recombinant or purified proteins.<\/li>\n\n\n\n<li>Assess protein heterogeneity.<\/li>\n\n\n\n<li>Determine the&nbsp;drug-to-antibody ratio (DAR)&nbsp;for antibody-drug conjugates (ADCs).<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">User provides:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>A purified protein solution.  Recommended protein concentration:&nbsp;1\u201320 mg\/mL.<\/li>\n\n\n\n<li>Samples should be free of nonvolatile contaminants and surfactants (e.g.,&nbsp;SDS, Triton X-100, NP-40, Tween-20\/80, PEG, and similar detergents), which interfere with mass spectrometric analysis.<\/li>\n\n\n\n<li>Recommended sample purity:&nbsp;\u226570%, as assessed by SDS-PAGE or an equivalent method.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Service performed:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Samples are analyzed by reversed-phase UHPLC coupled to high-resolution mass spectrometry using a&nbsp;Thermo Scientific Vanquish Horizon UHPLC&nbsp;and&nbsp;an Orbitrap Exploris 480&nbsp;mass spectrometer.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Report details:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Measured intact molecular mass<\/li>\n\n\n\n<li>Mass accuracy (mass error)<\/li>\n\n\n\n<li>Charge state distribution<\/li>\n\n\n\n<li>Deconvoluted mass spectrum<\/li>\n\n\n\n<li>Relative abundance of detected mass species<\/li>\n\n\n\n<li>Drug-to-antibody ratio (DAR), when applicable<\/li>\n\n\n\n<li>Relative abundance of different glycoforms and other protein variants, when applicable<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/Sample_intact_mass_analysis_report.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">SAMPLE REPORT<\/a><\/strong><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Cost:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Intact protein mass analysis:<\/strong>  <\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>$100\/sample (NC State Internal rate)<\/li>\n\n\n\n<li>$152\/sample (External academic or federally funded clients rate)<\/li>\n\n\n\n<li>$500\/sample (Commercial rate).<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Top-down protein sequencing:<\/strong>  <\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>$125\/sample (NC State Internal rate)<\/li>\n\n\n\n<li>$190\/sample (External academic or federally funded clients rate)<\/li>\n\n\n\n<li>$600\/sample (Commercial rate).<\/li>\n<\/ul>\n\n\n<div class=\"ncst-askew-media-text has-custombg-two-background-color wp-block-ncst-mini-story\">\n    <div class=\"ncst-askew-media-text__container\">\n      \n<div class=\"wp-block-ncst-text-column\">\n    <h2 class=\"ncst-text-column__heading\">Interactome Analysis (pull-downs)<\/h2>\n    <p class=\"ncst-text-column__teaser\">Identification of binding partners from AP\/MS (Affinity Purification) or Co-IP assays to elucidate protein-protein networks<\/p>\n          \n<div class=\"is-text wp-block-ncst-buttons\">\n    \n<div class=\"is-style-secondary wp-block-ncst-button\">\n      <a\n        class=\"ncst-block__button-link btn\"\n        href=\"mailto:qshu@ncsu.edu?cc=Taufika_Williams@ncsu.edu&amp;subject=Interactome%20Analysis\"\n        data-ncst-lightbox=\"false\"\n                      >\n                  <span class=\"text\">Questions? Contact us!<\/span><span class=\"arrow-indicator\"><svg class=\"wolficon wolficon-arrow-right-bold\" role=\"img\"  aria-hidden=\"true\">\n\t\t\t\n\t\t\t<use xlink:href=\"#wolficon-arrow-right-bold\">\n\t\t<\/svg><\/span>\n              <\/a>\n    <\/div>\n  \n\n  <\/div>\n\n\n      <\/div>\n\n\n<div class=\"wp-block-ncst-media\">\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"576\" src=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/IP-MS-1024x576.jpg\" alt=\"Protein interactions pull-down workflow.\" class=\"wp-image-2693\" srcset=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/IP-MS-1024x576.jpg 1024w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/IP-MS-300x169.jpg 300w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/IP-MS-768x432.jpg 768w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/06\/IP-MS.jpg 1500w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n<\/div>\n\n    <\/div>\n  <\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Description:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Identify protein binding partners from&nbsp;<strong>affinity purification (AP-MS)<\/strong>&nbsp;or&nbsp;<strong>co-immunoprecipitation (Co-IP)<\/strong>&nbsp;experiments using quantitative LC-MS\/MS. This service is designed to characterize protein-protein interactions by identifying proteins specifically enriched with a target (bait) protein.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">User provides:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Samples prepared according to our <a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/Standard-immunoprecipitation-coupled-to-MS-IP-MS.pdf\"><strong>sample <\/strong><\/a><strong><a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/Standard-immunoprecipitation-coupled-to-MS-IP-MS.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">submission<\/a><\/strong><a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/Standard-immunoprecipitation-coupled-to-MS-IP-MS.pdf\"><strong> guidelines<\/strong>.<\/a><\/li>\n\n\n\n<li>Appropriate&nbsp;<strong>negative controls<\/strong>&nbsp;(required) to distinguish specific interactors from nonspecific background. Examples include:<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list is-style-subdued-list\">\n<li>IgG isotype control<\/li>\n\n\n\n<li>Tag-only control<\/li>\n\n\n\n<li>EGFP-tag control<\/li>\n\n\n\n<li>Other appropriate experimental controls<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The&nbsp;<strong>species<\/strong>&nbsp;from which the samples were derived or, if applicable, a custom protein sequence database (FASTA format).<\/li>\n\n\n\n<li>The amino acid sequence or accession number of the&nbsp;bait protein, if it is not present in the reference database.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Service performed:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Samples are analyzed by nanoLC-MS\/MS using a&nbsp;Thermo Scientific Orbitrap Eclipse Tribrid&nbsp;mass spectrometer. Protein identification is performed using&nbsp;Proteome Discoverer&nbsp;with database searching against the appropriate protein sequence database. Quantitative comparison of experimental and control samples is used to identify proteins that are&nbsp;significantly enriched&nbsp;with the bait protein, generating a list of&nbsp;candidate binding partners.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Report details:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Identified proteins<\/li>\n\n\n\n<li>Peptide sequences<\/li>\n\n\n\n<li>Peptide-spectrum matches (PSMs)<\/li>\n\n\n\n<li>Protein sequence coverage<\/li>\n\n\n\n<li>Relative protein abundance across experimental and control samples<\/li>\n\n\n\n<li>Statistical enrichment analysis of proteins in bait versus control samples<\/li>\n\n\n\n<li>List of candidate binding partners<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>SAMPLE REPORT<\/strong> AVAILABLE UPON REQUEST<\/h4>\n\n\n\n<h3 class=\"wp-block-heading\">Cost:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Exploratory Analysis:<\/strong>  (one experimental &amp; one control sample; not publishable)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>$350 \/ experiment (NC State Internal rate)<\/li>\n\n\n\n<li>$532 \/ experiment (External academic or federally funded clients rate)<\/li>\n\n\n\n<li>$1750 \/ experiment (Commercial rate).<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Full Analysis: <\/strong>(three experimental &amp; three control samples; generally suitable for publication)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>$1000 \/ experiment (NC State Internal rate)<\/li>\n\n\n\n<li>$1520 \/experiment (External academic or federally funded clients rate)<\/li>\n\n\n\n<li>$5000\/ experiment (Commercial rate).<\/li>\n<\/ul>\n\n\n<div class=\"ncst-askew-media-text has-custombg-two-background-color mirror-layout wp-block-ncst-mini-story\">\n    <div class=\"ncst-askew-media-text__container\">\n      \n<div class=\"wp-block-ncst-text-column\">\n    <h2 class=\"ncst-text-column__heading\">Comparative Quantitative Proteomics <\/h2>\n    <p class=\"ncst-text-column__teaser\">By digesting proteins into peptides and measuring their relative signal intensities through LC-MS\/MS, researchers can quantify and compare the abundance of thousands of proteins across two samples to identify significant biological shifts.<\/p>\n          \n<div class=\"is-text wp-block-ncst-buttons\">\n    \n<div class=\"is-style-secondary wp-block-ncst-button\">\n      <a\n        class=\"ncst-block__button-link btn\"\n        href=\"mailto:qshu@ncsu.edu?cc=Taufika_Williams@ncsu.edu&amp;subject=Comparative%20Quantitative%20Proteomics\"\n        data-ncst-lightbox=\"false\"\n                      >\n                  <span class=\"text\">Questions? Contact us!<\/span><span class=\"arrow-indicator\"><svg class=\"wolficon wolficon-arrow-right-bold\" role=\"img\"  aria-hidden=\"true\">\n\t\t\t\n\t\t\t<use xlink:href=\"#wolficon-arrow-right-bold\">\n\t\t<\/svg><\/span>\n              <\/a>\n    <\/div>\n  \n\n  <\/div>\n\n\n      <\/div>\n\n\n<div class=\"wp-block-ncst-media\">\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"512\" src=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/04\/Eclipse-1024x512.jpg\" alt=\"Thermo Eclipse\" class=\"wp-image-2069\" srcset=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/04\/Eclipse-1024x512.jpg 1024w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/04\/Eclipse-300x150.jpg 300w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/04\/Eclipse-768x384.jpg 768w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/04\/Eclipse-1536x768.jpg 1536w, https:\/\/research.ncsu.edu\/metric\/files\/2026\/04\/Eclipse.jpg 1600w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n<\/div>\n\n    <\/div>\n  <\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Description:<\/h3>\n\n\n<p class=\"is-style-statement\">\n<p data-path-to-node=\"6\" style=\"white-space: normal; caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);\">Compare protein abundance across biological samples using state-of-the-art\u00a0<b data-path-to-node=\"6\" data-index-in-node=\"75\">label-free quantitative LC-MS\/MS (LFQ)<\/b>. This service enables the high-throughput identification and quantification of thousands of proteins, allowing investigators to pinpoint differentially expressed proteins between distinct experimental conditions.<\/p>\n<\/p>\n\n\n<p class=\"wp-block-paragraph\"><span style=\"font-size: var(--body-size); caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); white-space: normal;\">\u26a0\ufe0f&nbsp;<\/span><strong>Experimental Design Note:<\/strong>&nbsp;For statistically robust data, we require a minimum of&nbsp;<strong>three (3) <\/strong>biological replicates&nbsp;per experimental group.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">User provides:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Protein Samples:<\/strong>&nbsp;5\u201310 \u00b5g of purified protein per sample, prepared according to our <a href=\"https:\/\/research.ncsu.edu\/metric\/files\/2026\/07\/METRIC-SP3-Bottom-up-Proteomics.pdf\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Sample Preparation Guidelines<\/strong>.<\/a><\/li>\n\n\n\n<li><strong>Experimental Metadata:<\/strong>&nbsp;A detailed description of the experimental design, including sample groups, control groups, and biological replicates.<\/li>\n\n\n\n<li><strong>Sequence Database:<\/strong>&nbsp;The specific&nbsp;species&nbsp;of origin or a custom protein sequence database in&nbsp;FASTA format&nbsp;(if applicable).<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Service performed:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Mass Spectrometry:<\/strong>&nbsp;Peptides are analyzed via nanoLC-MS\/MS on a&nbsp;Thermo Scientific\u2122 Orbitrap Eclipse\u2122 Tribrid\u2122&nbsp;mass spectrometer using Data-Independent Acquisition (DIA).<\/li>\n\n\n\n<li><strong>Data Processing:<\/strong>&nbsp;Protein identification and label-free quantification (LFQ) are performed using&nbsp;Proteome Discoverer\u2122.<\/li>\n\n\n\n<li><strong>Statistical Analysis:<\/strong>&nbsp;Differential abundance is calculated using tailored statistical methods (e.g., pairwise comparisons or multi-group ANOVA) based on your experimental design.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Report details:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Differential Expression Analysis:<\/strong>&nbsp;Fold-changes between experimental groups alongside statistical significance metrics (adjusted&nbsp;<em>p<\/em>-values and False Discovery Rate).<\/li>\n\n\n\n<li><strong>Protein Identification &amp; Coverage:<\/strong>&nbsp;Lists of identified proteins, sequence coverage, and peptide-spectrum matches (PSMs).<\/li>\n\n\n\n<li><strong>Quantification Data:<\/strong>&nbsp;Relative protein abundances across all samples, including identified peptide modifications where applicable.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><strong>SAMPLE REPORT<\/strong> AVAILABLE UPON REQUEST<\/strong><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Cost:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Exploratory Analysis:<\/strong>  (one experimental &amp; one control sample; not publishable)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>$500 \/ experiment (NC State Internal rate)<\/li>\n\n\n\n<li>$760 \/ experiment (External academic or federally funded clients rate)<\/li>\n\n\n\n<li>$2500\/ experiment (Commercial rate).<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Full Analysis: <\/strong>(three experimental &amp; three control samples; generally suitable for publication)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>$1500 \/ experiment (NC State Internal rate)<\/li>\n\n\n\n<li>$2280 \/experiment (External academic or federally funded clients rate)<\/li>\n\n\n\n<li>$7500\/ experiment (Commercial rate).<\/li>\n<\/ul>\n\n\n<div class=\"has-custombg-two-background-color wp-block-ncst-button-spotlight\">\n    <div class=\"button-spotlight__container\">\n          <div class=\"button-spotlight__icon-container ncst-icon\">\n          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16.2188L19.0077 15.5949Z\" fill=\"currentColor\" \/><\/svg>\n\n      <\/div>\n        <div class='button-spotlight__content-container'>\n      <h2 class=\"button-spotlight__heading\">Acknowledging METRIC<\/h2>\n              <p class=\"button-spotlight__support\">To ensure the continued support and visibility of METRIC, please cite the facility in all scholarly outputs\u2014including publications, theses, dissertations, and presentations\u2014that utilize data collected at METRIC facilities.<\/p>\n            \n<div class=\"is-style-secondary wp-block-ncst-button\">\n      <a\n        class=\"ncst-block__button-link btn\"\n        href=\"https:\/\/research.ncsu.edu\/metric\/getting-started\/citing-metric\/\"\n        data-ncst-lightbox=\"false\"\n                      >\n                  <span class=\"text\">Citing METRIC<\/span><span class=\"arrow-indicator\"><svg class=\"wolficon wolficon-arrow-right-bold\" role=\"img\"  aria-hidden=\"true\">\n\t\t\t\n\t\t\t<use 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This service can be used to: User provides: Service performed: Peptide samples are analyzed by nanoLC-MS\/MS on a&hellip;<\/p>\n","protected":false},"author":243,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"ncst_custom_author":"","ncst_show_custom_author":false,"ncst_dynamicHeaderBlockName":"ncst\/default-header","ncst_dynamicHeaderData":"{\"pageIntro\":\"Our goal is to provide expert analytical services to North Carolina State University researchers at a cost-effective rate using state-of-the-art instrumentation.\"}","ncst_content_audit_freq":"","ncst_content_audit_date":"","ncst_content_audit_display":false,"ncst_backToTopFlag":"","footnotes":""},"tags":[],"class_list":["post-2209","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Proteomics &amp; Protein Characterization - METRIC<\/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:\/\/research.ncsu.edu\/metric\/proteomics-protein-characterization\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Proteomics &amp; Protein Characterization - METRIC\" \/>\n<meta property=\"og:description\" content=\"Description: Identify proteins in solution or in excised gel bands using nanoLC-MS\/MS. 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