Collaboration FAQs

What is the Broad Proteomics Platform?

The Broad Proteomics Platform is a center of collaboration and technology innovation center providing end-to-end mass spectrometry–based proteomics solutions for discovery and translational research. Our team includes Ph.D.-level scientists, research associates and computational biologists with deep expertise in analytical chemistry, biology and bioinformatics. We collaborate closely with internal and external investigators to design, execute and interpret proteomics experiments across a wide range of applications.

What technologies and methods are available in the Proteomics Platform?

Our Platform offers a broad range of state-of-the-art proteomics capabilities, including:

• Global and quantitative proteome profiling (TMT, label free DIA/DDA)
• Phosphoproteomics and other PTM analyses
• Affinity purification–mass spectrometry (AP–MS, TurboID, APEX)
• Immunopeptidomics (HLA-I and HLA-II)
• Drug target identification by thermal profiling and limited proteolysis (PISA/PELSA)
• Cell-surface proteomics
• Targeted MS for biology and preclinical validation assays (PRM, SRM)
• Structural analysis (HDX-MS, cross-linking MS)
• Spatial proteomics  (FFPE/ fresh frozen tissue)
• Secretome and exosome analyses
• Plasma Proteomics
• Computational and statistical analyses

How does the Platform engage with collaborators?

As with all Broad Platforms, we act as scientific partners, not service providers.
We engage deeply at every stage, from project conception and experimental design to data generation, analysis, and publication. Our scientists share expertise, discuss potential pitfalls, and guide optimization strategies that can be critical for success. Continued collaboration ensures your project benefits from state-of-the-art instrumentation and methods often developed and validated within our team before publication.

How can I initiate a collaboration?

Email scarr@broadinstitute.org and udeshi@broadinstitute.org with a brief description of your project and goals. We will connect with you for an introductory discussion to determine the best path forward.

When we meet, please come prepared to discuss the following:

• Overall goal: What biological, clinical or mechanistic question do you hope proteomics will address?
   
• Model system: What organism, cell type or tissue are you studying?
• Sample details: Number of samples, approximate amount of material, and how they were prepared or stored (e.g., frozen tissue, cell pellets, lysates).
• Analysis needs: What level of bioinformatics or data interpretation support will you require?

What if my project is still early in development?

That’s perfectly fine. We routinely meet with investigators at all stages from exploratory discussions about feasibility and study design to advanced collaborations involving complex datasets. Early engagement often helps optimize sample collection, experimental design and resource planning.

Who can access Broad Proteomics capabilities?

We collaborate with Broad Institute researchers, Broad-affiliated labs, and external academic and industry partners through collaborative projects, consortia and sponsored research agreements.

What happens after the introductory meeting?

If the project is appropriate for our group to take on, then after our meeting. You will fill out a Proteomics Collaboration Form so a quote can be generated for the work. 

• We may recommend a small scale pilot project to evaluate feasibility. In this case you will still fill out a Proteomics Collaboration Form so a quote can be generated for the pilot work. 
• For unfunded projects or novel capabilities, forging an academic collaboration, usually in the form of a grant application. 

For collaboration projects, a Platform scientist/s will work with you for consultation, analysis and manuscript writing, as needed. We encourage you to reach out with questions as they arise, whether strategic or technical. It is nearly always easier to advise or troubleshoot through regular communication rather than after the project is already long underway.

How much will my project cost?

The cost of work varies depending on the complexity of the effort, the amount of instrument time, cost of reagents and extent of advanced data analysis required. Costs can range from $2000 to $50,000+ depending on these factors. 

How are costs determined?

We operate as a specialized service facility (SSF) that makes the recovery of our costs fair and equitable and allows investment for future process improvements.  The SSF designation allows costs to be separately allocated for the purpose of determining a total charge for a specific activity. The total charge is a price per unit based on the accumulated direct costs for each SSF activity (personnel, materials, equipment maintenance, other charges, and depreciation of equipment) as well as the indirect costs in support of the activities. These latter costs are determined by the allocation of departmental administration, central administration, and facilities operations including rent, utilities and maintenance attributed to the SSF.

Are discounts available for Broad affiliates?

Unfortunately, we cannot offer discounts to anyone, regardless of their affiliation. SSF prices are set at a rate that covers the labor, materials, and indirect costs of the particular assay, with no profit margin.

How does authorship work?

When Proteomics Platform scientists provide their intellectual expertise and technical skills, they should be included at the appropriate level of attribution as with any other key collaborator. 

What is your policy on sample re-runs? 

If we made a processing error that results in the failure of an assay then we will re-run the sample at no additional cost. If a sample needs to be reanalyzed for other reasons (e.g. poor sample quality) then the cost of the reanalysis is the investigator’s responsibility.

I have an active IRB (Internal Review Board) application at my home institution. Does my IRB have to be approved at the Broad? 

Yes. This is required of all human samples that will be undergoing genetic analysis at the Broad. The Proteomics manager here at the Broad will work with you to complete the proper forms needed to obtain approval from the Broad’s IRB. Please note that we must have IRB approval of your project before your samples can be analyzed.

What happens if I have an active IRB application at the Broad?

The IRB approval must include proteomic testing in the protocol before testing can begin. To ensure the IRB approval covers proteomics testing we will work with you to complete the proper forms needed to add your project to our comprehensive exempt protocol or amend your protocol to include proteomics testing.