Skip to main content
 

About

The Metabolomics and Proteomics (MAP) Core offers an array of metabolomics and proteomics services for a variety of sample types including biofluids, cells, and tissues.  The MAP Core also specializes in method development and provides expert consultation on experimental design. The MAP Core is well-staffed with eight highly trained team members, and is equipped with seven state-of-the-art mass spectrometry systems: Thermo Exploris240, Thermo Stellar, Thermo Fusion Lumos Tribrid, Thermo QExactive HF, Two Thermo Exploris480, and a Thermo Astral. The Core is also outfitted with a Thermo Ultimate3000, three Thermo Easy nLC 1200s, an Evosep One, a Vanquish Neo UHPLC, three Vanquish Horizon UHPLC, and a 908 Devices ZipChip capillary electrophoresis device for up-front separation. The Core has an Agilent 1260 Infinity II HPLC for offline peptide fractionation and is now equipped with a Thermo AccelerOme for automated high-throughput sample preparation.

For more information about core services and rates, visit the MAP Cores website.

The MAP Core is an exciting new collaboration between the UNC NORC, UNC School of Medicine, and Lineberger Comprehensive Cancer Center. The Core is housed within the Department of Pharmacology in UNC’s School of Medicine.

Core Directors

Laura Herring, PhD

Director, MAP Core
Associate Professor of Pharmacology
+1 (919) 966-4681
laura_herring@med.unc.edu

 

 


Whitney Stutts, PhD

Associate Director of Metabolomics
Associate Professor of Pharmacology
+1 (919) 600-0000
wlstutts@email.unc.edu

Services

Proteomics – LC-MS/ MS Services:

Protein identification, in-gel

A highly purified protein, visible by Coomassie, is submitted in-gel; most abundant protein(s) can be detected.

Post-translational modification (PTM) site mapping

Identification/localization of PTMs on purified proteins, which can be submitted either in-gel or in-solution. Examples of PTMs include: Phosphorylation, ubiquitination, acetylation, methylation and glycosylation. If you’re interested in a specific modification, please contact us so that we may direct you to sample preparation protocols that could be used to optimize its detection.

To confirm PTMs on specific residues, please contact the MAP Core staff. We may be able to use targeted methods to specifically look for the peptide containing the PTM of interest.

Protein characterization

This service can include the following types of analyses:

  1. Identification of other types of covalent modifications besides PTMs, such as a drug or other compound. The customer must provide us with the compound formula of these modifications.
  2. Identification/confirmation of a mutated amino acid, dependent on location of mutated amino acid.
  3. Identification/confirmation of truncated protein, dependent on protein sequence.

Proteomic profiling

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. Quantitation allows measurement of the relative changes in protein abundances between controls and samples to identify significantly regulated proteins. TMT-based or label-free quantitation is available.

Post-translational modification (PTM) profiling

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, > 20,000 phospho sites can be detected.

Additional PTMs such as ubiquitylation, acetylation, and methylation (using Cell Signaling Technology’s antibody-based kits) can also be profiled on a global level.

Affinity purification-mass spectrometry (AP-MS) analysis

Identification of protein binding partners of proteins captured using affinity purification techniques (including endogenous, overexpressed, proximity labeled, DNA, RNA, drug pulldowns, etc). 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.

Multiplex inhibitor bead coupled to mass spectrometry (MIB-MS) kinome profiling

This service is performed in collaboration with Dr. Lee Graves’ lab, please contact him with inquiries. Immobilized pan kinase inhibitors are used to capture kinases from a complex sample. Over 200 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.

Targeted analysis

Analysis by LC-MS/MS using targeted methods to confirm and/or quantify a specific analyte of interest such as the detection of proteins/peptides of interest in a complex sample. For this, parallel reaction monitoing (PRM) acquisition mode is commonly used on our mass spectrometers. If applicable, synthetic peptides can be used for detection and/or absolute quantitation and must be provided by the customer.

*Informatics*

The MAP Core provides initial data analysis including: Peptide/proteins identification/quantification using a variety of software packages including: Spectronaut (label-free DIA), Proteome Discoverer (TMT, label-free DDA), MaxQuant (label-free DDA), Spectrodive (targeted proteomics), or Skyline (targeted proteomics). 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.

Proteomics – High Resolution Intact Mass Analysis

Typically performed using  capillary electrophoresis coupled to mass spectrometry, using the ZipChip (908Devices). Protein or peptides are submitted lyophilized or in-solution, please contact us for buffer and concentration requirements. Intact molecular weight can be determined with high mass accuracy (ppm level) using one of our Orbitrap (high resolution) instruments. This service is used when high mass accuracy of a protein is needed, such as confirmation of a PTM or other modification.

Metabolomics

Broad Metabolite Panel

The MAP Core now offers a broad metabolite panel consisting of ~275 metabolites using 908Devices ZipChip capillary electrophoresis coupled to mass spectrometry. This novel, kit-based approach is an end-to-end workflow encompassing extraction, standards and QCs, as well as an automated quantitative data processing solution.

Please email the MAP Core’s Associate Director-Metabolomics, Whitney Stutts for more information on this and other assays coming soon.

Contact

Laura Herring, PhD

Director, MAP Core

120 Mason Farm Road
Chapel Hill, NC 27599


laura_herring@med.unc.edu

Metabolomics and Proteomics (MAP) Core