Proteomics: Services

VBRN Webinar: From Basic to Advanced Proteomic Applications and How They Might Benefit Your Research
October 12, 2017

Presented by Dr. Wai Lam, Proteomics Core Director. The question and answer session from the webinar begins at 29:00. For proteomics research consultations, please contact Dr. Wai Lam ( Future webinar topic suggestions can be emailed to Dr. Tabitha Finch (

University of Vermont Proteomics Core Facility: Current and Future Capabilities & Services

Current Proteomics Facility Capabilities

Protein identification and isoform characterization

De novo sequencing of novel proteins

Identification of protein-protein interacting partners / Quantitative interactomes

Identification of post-translational modifications (PTMs)

Peptide fractionation of complex mixtures

  • Off-line peptide separation (e.g., SCX)
  • Strong cation exchange fractionation
  • High-pH reverse phase fractionation
  • Phospho-peptide enrichment (e.g.,IMAC, TiO2, P-Tyr-100)
  • Acetylated peptide enrichment (e.g., PTMScan Acetyl-Lys Motif (Ac-K))

Enrichment of post-translationally modified peptides from complex mixtures:

  • Phosphopeptide enrichment (e.g., IMAC, TiO2, P-Tyr-100 Ab, 4G10 Ab, p-PKA substrate Ab)
  • Acetylated peptide enrichment (e.g., PTMScan Acetyl-Lys Motif (Ac-K))

Large-scale quantitative proteomics using stable isotopes

  • Stable Isotope Labeling by Amino acids in Cell culture (SILAC)
  • Dimethyl Labeling
  • Tandem Mass Tags

Absolute quantification of proteins using stable isotopically labeled standards.

Quantification of target peptides using Parallel Reaction Monitoring and Skyline

Identification and quantification of specific peptides from target proteins using selected ion monitoring.

Analysis of isotope-coded cross-linked peptides for structural proteomics

Please contact the facility personnel regarding the turnaround time for each type of analysis.

VBRN Proteomics Facility—Pricing

Below is the pricing for UVM/VBRN proteomics services.  Please contact VBRN directly to discuss your needs (

Software capabilities/Data Science support



Proteome Discover 2.5 (3 copies) with: SEQUEST, MASCOT and Byonic search engines

Protein identification/Quantitative proteomics.

Protein classification / Ontology.

SCAFFOLD Q+S (Proteome Software)


Evaluation of multiple mass spectrometry datasets (e.g. SILAC).

PEAKS Studio (Bioinformatics Solutions).

De novo sequencing.

HD Examiner

Hydrogen deuterium exchange experiments

We work closely with the VBRN Data Science Core to develop a comprehensive bioinformatics solution for our large-scale proteomics analyses, with the goal of streamlining the workflow from data collection, management and analysis, all the way to delivering results to investigators in a user-friendly format.

Future Proteomics Facility Capabilities

The VBRN facility continues to establish additional proteomics techniques, which are expected to be available in INBRE IV.  These method developments target areas that are carefully assessed by the facility personnel as the future needs from the investigators at UVM and BPIs.

Future Proteomics Facility Capabilities

Mass spectrometry analysis of isotope-coded cross-linked peptides for structural proteomics.

Hydrogen-deuterium exchange mass spectrometry


Acknowledging Core Facilities in Research Publications (

Recommended Guidelines for Authorship on Manuscripts (