Division of Biology and Medicine
BioMed Core Facilities

Proteomics Facility

The Proteomics Core provides protein and proteomic analysis instrumentation for protein identification, characterization, and quantification.


The Proteomics Core Facility's mission is to provide well-maintained, state-of-the-art instrumentation and fundamental proteomics expertise to Brown University and the Rhode Island scientific community. We aim to be a focal point of intellectual activity in proteomics by enabling nationally recognized proteomics research within Rhode Island. The Proteomics Core Facility provides training in emerging proteomic techniques and has a strong commitment to be at the leading edge of current and developing technologies and provide consultation on their application.  We welcome inquiries from scientists and teachers seeking information regarding how we may assist them in furthering their research and educational goals.



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Services and Instruments

Description of Services

♦  Includes protein digestion, desalting, and LC/MS analysis. .raw files are the only deliverable.

♦  Includes what is offered in Basic Service with the deliverable being an Excel report of Protein IDs and % Abundance from MaxQuant.

♦  Includes what is offered in Complete Service with the additional step of TiO2 phosphopeptide enrichment and data analysis with MaxQuant. The deliverable will be an excel file with phosphopeptide site analysis.

Custom Development
♦  Billed hourly and may consist of extra data analysis (volcano plots, heat maps, etc), developing a PRM method, Analytical Development, and optimizing digestion with specific or difficult samples.


Sample numbers should be determined based on power analysis or expected magnitude of protein changes group to group. Otherwise, 4 samples per group are highly recommended.

Gel bands (Coomassie and Silver stained) for protein identification will be rejected unless they are cubed (~1mm) in 1.5mL centrifuge tubes and destained.

For Immunoprecipitation, Pull-down, or Interactomic studies:

  • Sample numbers should be at least n=4 or more and require at least 200ug of just protein (not beads).
  • IP and pull-downs should be eluted with 5%SDS and 50mM Triethylammonium Bicarbonate Buffer (pH 8.5).
  • The sequence of the bait protein must be included in FASTA file.
  • IP antibody control (i.e. non-specific binding control with no antibody) must be included. 

Failure to include any of these will result in delays in data analysis and additional charges.

Total protein concentration must be determined prior to tendering samples to the core for analysis. A detergent-compatible BCA is highly recommended and concentrations must be noted in the Sample Manifest File in addition to how samples should be grouped.

Sample Workflow


Service Request and Reservations

E-mail Nicholas_DaSilva@brown.edu to reserve time on the Q Exactive Mass Spec.


Please note, the following biophysics instruments are now managed under the Structural Biology Core:

  • Fluoromax - 4

  • Jasco J-815

  • Nanodrop 8000

  • Microcal Isothermal Titration

  • Microcal VPViewer

  • Nanotemper MST



FY24 Rates


Service Units Internal Academic Rates* External Academic Rates
Q Exactive Basic Service Sample $82 $131
Q Exactive Complete Service Sample $134 $213
Q Exactive Phosphoproteomic Services Sample $175 $279
Q Exactive Self Use Sample $41 $65
Custom Service Development Hour $78 $124

*Rates for Brown and Rhode Island Academic Institutions and Hospital Affiliates

Rates Effective 1/1/2024


Facility Manager


Rhode Island NSF/EPSCoR Center for Proteomics
Brown University
Laboratories of Molecular Medicine
70 Ship Street, Room 339
Providence, RI, 02903


Laboratories for Molecular Medicine
70 Ship Street
Providence, RI 02903 

MapQuest Directions to the Laboratories for Molecular Medicine 

Campus Map:
70 Ship Street
Providence, RI 02903

LMM Building: Jewelry District- Downtown Providence

Related Links:

Resources for Grants

Proteomics Core Facility. The proteomics facility, located at the Laboratories for Molecular Medicine, is directed and staffed by a PhD-level scientist. Facility instrumentation includes a Thermo Scientific Q Exactive™ Hybrid Quadrupole-Orbitrap Mass Spectrometer, a Jasco J-815 Circular Dichroism Spectrometer, MicroCal VP Differential Scanning Calorimeter, a MicroCal Isothermal Titration Calorimetry iTC200, HORIBA Jobin Yvon FluoroMax-4 Spectrofluorometer.

Scientific reproducibility is enhanced through scientific rigor and transparency.  Scientific rigor is the strict application of the scientific method to ensure unbiased and well-controlled experimental design, methodology, analysis, interpretation, and reporting of results. The Proteomics Facility is committed to supporting research excellence by adopting the following practices of scientific rigor.

  • Purchase and maintain a variety of high-quality instruments from established vendors such that the best instrument is available for any given research analysis.
  • The equipment is overseen by highly trained Proteomics Facility experts and is well maintained under service contracts or funds budgeted for annual preventive maintenance and repairs.
  • The Proteomics experts are available for experimental design consults or troubleshooting.
  • All Proteomics Facility users are thoroughly trained by the expert staff, one on one, and not granted access to the instruments until they are deemed to be suitably trained. 
  • All newly trained users are also required to use the Proteomics instruments during daytime hours to increase interaction with the expert staff members.


This facility was supported in part by grants from the National Institutes of Health (NIH), the National Science Foundation (NSF), Brown University's Division of Biology and Medicine and Provost's office.

We request that users of our facility please use this statement when acknowledging work performed in the facility:

"This research is based in part upon work conducted using the Rhode Island NSF/EPSCoR Proteomics Share Resource Facility, which was supported in part by the National Science Foundation EPSCoR Grant No. 1004057, National Institutes of Health Grant No. 1S10RR020923, S10RR027027 (Orbitrap XL ETD Mass Spectrometer), a Rhode Island Science and Technology Advisory Council grant, and the Division of Biology and Medicine, Brown University."