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.
Proteomics Facility
The Proteomics Core provides protein and proteomic analysis instrumentation for protein identification, characterization, and quantification.
About
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.
Find us at CoresRI!
Services and Instruments
Description of Services
Basic
♦ Includes protein digestion, desalting, and LC/MS analysis. Thermo .raw files are the
only deliverable.
Complete – Protein Profiling
♦ Includes what is offered in Basic Service with the deliverable being an Excel report of
Protein IDs and % Abundance from Spectromine/Spectronaut/Proteome
Discoverer/MaxQuant where appropriate. All users select this option for protein profiling,
unenriched PTM analysis, and label free quantitation projects.
Complete – Co-IP Interactomics
♦ Includes what is offered in Basic Service with additional sample cleanup, an Excel
report of IP unique Protein IDs, % Abundance, and basic networking analysis .
Phosphoproteomics
♦ Includes what is offered in Complete Service with the additional step of TiO2
phosphopeptide enrichment and PTM localization or site analysis from Proteome
Discoverer/Spectronaut/Spectromine. The deliverable will be an excel file with
phosphopeptide site analysis.
Custom Development
♦ Billed hourly and may consist of developing a PRM method, Analytical Development,
and optimizing digestion with specific or difficult samples.
TMT Multiplex Profiling Services (Coming Soon)
♦ Digestion, TMT Labeling with Pooled mix of 10 samples, LC/MS analysis, and Excel report of
labeled quantities
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Guidelines
Sample numbers should be determined based on power analysis or expected
magnitude of protein changes group to group. Otherwise, 4 samples per group are
required. Pilot studies should contain at least 3 samples per test group.
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 optimized eluted with an appropriate mass spec friendly
buffer (e.g. 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 and additional charges.
For all projects, total protein concentration must be determined prior to tendering
samples to the core for analysis. A detergent-compatible BCA may be used and
concentrations must be noted in the Sample Manifest File when submitting a request via
iLabs in addition to specifying how samples should be grouped for analysis.
Failure to do so will result in delays and additional fees.
For all projects, total protein concentration must be determined prior to tendering
samples to the core for analysis. A detergent-compatible BCA may be used and
concentrations must be noted in the Sample Manifest File when submitting a request via
iLabs in addition to specifying how samples should be grouped for analysis.
Failure to do so will result in delays and additional fees. As a general rule, users should
aim to have a protein concentration in the range of approximately 0.5-6ug/uL.
Detergents in buffer are the major areas of concern for all users. Compatible
Detergents: 0.05%-12% SDS, 0.05%-0.5% CHAPS (sodium deoxycholate,
Triethylammonium bicarbonate are also MS friendly reagents). SDS based or mild
detergent buffers can be used with our SDS-Trap columns and SDS-based detergents
are recommended.
Incompatible Detergents/Buffer Components: Nonidet P-40 (which can no longer be
purchased; Sigma is substituting CAIgepal 630), Triton® X-100 (or any derivative),
Igepal/PEG (any derivative), Brij®-35 (or any derivative), Tween®-20, OTG, CHAPSO,
Type NP40/NP40 alternative.
Sample Workflow
Service Requests and Reservations
To request service, please go to Brown iLab
Login with your Brown credentials and select the Proteomics Core from the drop-down menu. Then click on “request services” and follow the instructions to initiate requests, reservations, and billing.
Rates
FY25 Rates
| Service | Units | Internal Academic Rates* | External Academic Rates | Commercial Rates |
|---|---|---|---|---|
| Q Exactive Complete Service | Sample | $113 | $180 | $287 |
| Ascend Basic Service | Sample | $106 | $169 | $270 |
| Ascend Complete Service - Protein Profiling | Sample | $238 | $379 | $605 |
| Ascend Complete Service - CoIP Interatomics | Sample | $325 | $518 | $827 |
| Ascend Phosphoproteomic Services | Sample | $224 | $357 | $570 |
| Ascend Self Use | Sample | $9 | $14 | $23 |
| TMT Multiplex Profiling Service | Mix (10 samples) | $1,624 | $2,590 | $4,131 |
| Custom Service Development | Hour | $82 | $130 | $208 |
*Rates for Brown and Rhode Island Academic Institutions and Hospital Affiliates
Rates Effective 11/18/2024
Contact/Location
Facility Manager
Location
Proteomics Core Facility
Brown University
Laboratories of Molecular Medicine
70 Ship Street, Room 410
Providence, RI, 02903
Directions
Laboratories for Molecular Medicine MapQuest Directions to the Laboratories for Molecular Medicine | Campus Map: LMM Building: Jewelry District- Downtown Providence | Related Links: |
Resources for Grants
The Proteomics Core Facility, located at the Laboratories for Molecular Medicine, is directed and staffed by a PhD-level scientist. Facility instrumentation includes a Thermo Scientific Ascend Tribrid Orbitrap Mass Spectrometer with a FAIMS Pro Duo Ion Mobility Interface and Vanquish Neo UHPLC. The core also operates a Thermo Scientific Q Exactive™ Hybrid Quadrupole-Orbitrap Mass Spectrometer with a Thermo Scientific/Dionex Ultimate 3000 UHPLC.
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.
Acknowledgment
This facility was supported in part by grants from the National Institutes of Health (NIH), 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 Proteomics Core Facility, which was supported in part by the National Institutes of Health Grant No. 1S10RR027027 (Orbitrap XL-ETD), 1S10OD036295 (Ascend Tribrid, FAIMS, Vanquish Neo), and the Division of Biology and Medicine, Brown University."