Thermo Fisher Scientific Proteomics Facility for Disease Target Discovery

How we work

We operate as a collaborative mass spectrometry facility associated with the laboratory of Nevan Krogan, the Quantitative Biosciences Institutes (QBI), and the Gladstone Institutes.  As such, we thrive on establishing collaborations in which we can leverage initial experiments to apply for collaborative funding opportunities.

Using this approach has enabled us to serve a fundamental role in many collaborative grants including:

Team Members

Our team has expertise in a wide variety of proteomic applications including:

  • Protein-protein interactions (PPIs)
  • Global analysis of protein abundance and post-translational modifications (phosphorylation, ubiquitylation, acetylation, etc.)
  • Targeted proteomics
  • Cross-linking mass spectrometry
  • Data-independent analysis (DIA)



We have a wide variety of instrumentation suitable for discovery and targeted proteomics experiments. 

Protocols & Resources

Here are some of our favorite protocols and software tools.


An overview of the types of experiments we routinely perform.

Collaborating Labs

We are fortunate to collaborate with dozens of labs in the UCSF community, and many beyond.

How to collaborate with our facility.

Collaborations are based upon shared interest in a biological or technological question.  Collaborations usually proceed as follows:

  1. Meeting to discuss scientific question of interest and gauge merit and feasibility of project.
  2. Small scale pilot experiment to establish feasibility in practice.
  3. Taking things to the next level:
    1. Proceed with larger project AND/OR
    2. Proceed with submitting application for collaborative funding
  4. Making this official:
    1. Secure funding to further pursue project AND/OR
    2. Publish collaborative paper

Interested in joining our team?

We are always in the market for motivated and talented people. If interested please send your CV/Resume to Danielle Swaney.

Currently we are actively looking for people with the following skills:

  • Postdoc mass with hands on mass spectrometry & proteomics expertise looking to develop new approaches, apply existing approaches to novel areas of biology, and/or pairing proteomics with our CRISPR-based functional genomics platforms.

Contact Information

Danielle Swaney

1650 Owens St

Gladstone Institutes

San Francisco, CA, 94158