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Mass Spectrometry Facility

The Mass Spectrometry Shared Resource provides services to elucidate the primary structure of novel proteins and to analyze protein/protein interactions, post-translational modifications and protein levels. The Resource also offers the ability to detect lipids, metabolites, and other small molecules. The equipment in the facility has been upgraded to provide state-of-the-art analysis using microcapillary LC-MS/MS on linear ion traps and Orbitraps, hybrid quadrupole-TOF mass spectrometers and MALDI-TOF.

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Shared Resource Staff

Research Associate

Keith Rivera


Arthur Makarenko

Facility staff is available to discuss project design and progress. Contact Keith Rivera to schedule an appointment. Services include:

  • Quantitative global proteomic profiling using iTRAQ and SILAC, including data analysis, merging of separate datasets and statistical treatment of results.
  • Quantitative cysteine profiling for global redox proteomics.
  • GSH/GSSG measurement (MRM) for redox assessment.
  • Multiple reaction monitoring (MRM) assays for:
    • Phosphatidylinositols (PIs) including head group, chain length, degree of saturation and phosphorylation state for 20 different PI lipid species.
    • Small molecule/drug measurement & clearance in serum & tissues (e.g. Clozapine and Clozapine N-Oxide, Vitamin C, Vitamin K).
  • Lipid Analysis, including sample preparation and extractions, MRM assay development, LC-MS/MS and data analysis.
  • Quantitative iTRAQ for protein complex IP.
  • Quantitative metabolite profiling of ~250 core metabolites.
  • Intact protein mass measurement for drug binding and to support crystallographic studies.
  • Training in LCMS and MS/MS, both for instrument operation and data analysis.
  • Consultation in experimental planning and customized experimental design.

The Shared Resource currently has four mass spectrometers in operation:

  • Thermo Scientific Linear ion trap-orbitrap (Velos Pro): iTRAQ screens, protein identification, protein complexes (iTRAQ), post-translational modification analysis (PTM, including phospho, acetyl, ubiquitination, glycosylation and oxidation).
  • Thermo Scientific Linear ion trap-orbitrap (XL): protein ID, PTM analysis and intact mass measurement.
  • Thermo Scientific Vantage Triple Quadrupole mass spectrometer (TSQ): peptide MRM, lipids, carbohydrates, small molecules & metabolites
  • Thermo Finnigan Linear ion trap (LTQ).

Sample preparation for the instruments is supported by a number of capillary liquid chromatography systems from Agilent and Proxeon.

Proteomics data is analyzed with the following data analysis packages:

  • Mascot and Mascot Integra
  • InSpecT
  • Scaffold

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