Accomplishments and discoveries from VGN students and faculty


VGN 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

Turnaround Time

Protein identification, isoform characterization (In-gel/In-solution digestion) and molecular weight determination.

1-2 weeks

Identification of protein-protein interacting partners and determination of binding stoichiometries (limited to < 200 proteins in a mixture).

1 week- 1 mo.

Identification of post-translational modifications (PTMs).

  • e.g., phosphorylation, N-glycosylation, methylation, acetylation, ubiquitination, tyrosine nitration, S-nitrosylation.

2-3 weeks

De novo sequencing of proteins

1 mo.

Peptide fractionation and enrichment from complex mixtures:

  • Off-line peptide separation (e.g., SCX).
  • Phospho-peptide enrichment (e.g.,IMAC, TiO2, P-Tyr-100, PTMScan, p-PKA Substrate).
  • Acetylated peptide enrichment (e.g., PTMScan Acetyl-Lys Motif (Ac-K).
  • Nitrosylated peptide enrichment (Biotin Switch Assay).

1 mo.

Quantitative Proteomics (with peptide fractionation/enrichment):

Mass spectrometry-based global quantification of protein expression and PTMs in biological samples using stable isotopes.

  • Isotope-coded affinity tags (ICAT).
  • Stable isotope labeling by amino acids in cell culture (SILAC).
  • Dimethyl labeling.

2 mo.

Absolute quantification of proteins using stable isotopically labeled standards.

1 mo.

Label-Free quantification (Spectral counting).

1 mo.

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

1 week-1 mo.

Structural elucidation of small molecules using liquid chromatography-high resolution/accurate mass (HR/AM) measurements and MSn.

1 week


As of June 2012, users are required to perform trypsin digestion before submitting their samples, but we will provide protocols and consultation.  Due to limited resources and the high volume of samples we have been receiving, the facility personnel are only able to allocate time to perform sample preparation for collaborative projects.

Other than routine protein identification, services that involve quantitative proteomics or targeted peptide analysis require significant amount of expertise/ time commitment from the facility personnel.  Therefore, we often work with investigators (especially users outside the University of Vermont) on a collaborative basis with an expectation of shared authorship in publications.    




Below is the pricing for UVM/VGN proteomics services.  However, should you find the prices prohibitive please contact VGN directly to discuss your needs (



Analysis of Digests:


Protein identification (gel band) - internal users:




Data Analysis/Interpretation:


                     Database searching - SEQUEST:


                     Database searching - Mascot:


                     Manual evaluation:


Peptide fractionation and enrichment (e.g., Immunoprecipitation):


Method Development (chemical derivatization of PTMs, etc):






We will guide investigators throughout the entire experiment(s), discuss the results, as well as provide assistance in manuscript preparations and future experiments.  According to specific goals of the experiments, facility personnel spend a significant amount of time analyzing the data with a suite of software or by manual inspection.  The facility has a Data Processing Center (Room 333) that houses three high-performance computers dedicated to proteomics data analysis.  A suite of software is currently implemented in our facility:



Proteome Discover 1.3 with SEQUEST and MASCOT (3 copies).

Protein identification/Quantitative proteomics.

Protein classification / Ontology.

SCAFFOLD Q+S (Proteome Software).

Evaluation of multiple MS datasets (e.g. SILAC).

SIEVE (Thermo Fisher Scientific).

Label-free quantification.

PEAKS Studio (Bioinformatics Solutions).

De novo sequencing.

SimGlycan (PREMIER Biosoft).

Glycopeptide analysis.

Protein Deconvolution (Thermo Fisher Scientific).

Intact protein analysis.

We work closely with the VGN Bioinformatics Core (directed by Dr. Fan Zhang) 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

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

Large-scale label-free quantification (SIEVE).

Characterization of peptides with increasingly complex glycosylation.

Characterization of peptides that are modified by unknown modification(s) or adducted by drug/small molecules.

Contact Information:

Vermont Genetics Network
University of Vermont
120A Marsh Life Science Building
Burlington, VT 05405-0086
(802) 656-9119
(802) 656-2914 - FAX

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