Mass Spectrometry and Proteomics Core

Overview of Services

The Johns Hopkins University (JHU) School of Medicine (SOM) Mass Spectrometry and Proteomics Facility assists investigators to identify and quantify proteins and their modifications that are differentially expressed in cells, tissues or body fluids, to track interactions with binding partners during changes in signal transduction, and to identify proteolytic cleavage sites and map post-translational modifications by providing the following proteomic services:

  • Consultation: Pre- and post-analysis.
  • Sample preparation: Buffer exchange; Column chromatography; Proteolytic digestion; Stable isotope labeling.
  • Protein Identification: Proteins in solution, in gel bands or spots, or in complex protein extracts.
  • Protein Modifications: A growing list of known and custom post translational modifications (PTMs) which include Acetylation, AMPylation, ADP ribosylation, citrullination, glycosylation, phosphorylation, proline hydroxylation, nitrosation, ubiquitination and novel cleavage sites, etc.
  • Protein Quantification:    Relative quantification: Multi-dimensional protein identification technology (MuDPIT), isobaric mass tags (TMTs) or stable isotopic amino acids (SILAC); Targeted Quantification: Parallel (PRM) Reaction Monitoring, Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM), and Protein Concentration ("Absolute Quantification") using standard peptides (AQUA) or recombinant proteins (PSAQ).
  • High Resolution Mass Analysis: Accurate mass of intact proteins; Characterization protein modifications.
  • Biostatical/Bioinformatic Analysis: PCA analysis, Volcano plots, Ingenuity based gene ontology pathway analysis; Bioinformatics consultation.
  • Training and Self-Service Equipment: In addition, the Core offers workshops to use the Core’s MALDI-TOF mass spectrometer, Typhoon gel imaging scanner and 2D gel electrophoresis equipment and proteomic software.


Director's Office:   512 Wood Basic Science Building (WBSB)
Staff Offices:         509 and 510 Hunterian Building (Hunt)
Research Labs:      503 and 504 WBSB
MALDI Lab:            511 Hunt
Phone Number:     410-614-6968


Operation: Monday through Friday, 9 am - 5 pm
Sample Drop off freezer at WBSB 503: available all week, all times

Sample Drop Off Protocol:
1. Label tubes with:  Tube number,  iLabs Service ID,  Sample Name
2. Place samples in an empty numbered rack in the core’s -20C freezer located outside WBSB 503.
3. Take a picture of your samples in the freezer rack.
4. Upload the picture to your project in iLabs. No picture, can’t start project.


Shipping Address

Dr. Robert Cole
Mass Spectrometry and Proteomics Facility
Department of Biological Chemistry, WBSB 512
Johns Hopkins School of Medicine
725 N. Wolfe St.
Baltimore, MD  21205

Links and Resources

  1. Mass Spectrometry and Proteomics Facility
  2. Scaffold Free Viewer
  3. Proteome Discoverer Free Viewer
  4. Peaks Free Viewer
  5. Byonics Free Viewer
  6. Skyline Free software
  7. Verify your Cancer Center Membership
  8. Verify your GI Center Membership


Name Role Phone Email Location
Robert N. Cole, PhD
WBSB 512
Tatiana N. Boronina, Ph.D.
Proteomics Specialist
Hunterian 509
Lauren R. DeVine, M.S.
Proteomics Specialist; Core Manager
Hunterian 510
Robert N. O'Meally, M.S.
Proteomics Specialist
Hunterian 510
Joshua W. Smith, PhD
Research Associate
Hunterian 509