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:


Applications

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

  • Protein-protein interactions (PPIs)

    • Affinity purification-mass spectrometry (APMS)

    • Proximity biotinylation (APEX, BioID, etc.)

    • Co-fractionation MS (SEC-MS)

  • Global proteomics analysis by label-free quantification (DDA or DIA)

    • Protein abundance

    • Post-translational modifications (PTMs): phosphorylation, ubiquitylation, acetylation, etc.

  • Targeted proteomics

  • Structural proteomics

    • Cross-linking mass spectrometry

    • Hydrogen-deuterium exchange (HDX-MS)

    • Native MS


How to collaborate with our facility.

Collaborations are based upon shared interest in a biological or technological question and 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

Instrumentation

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


Protocols & Resources

Here are some of our favorite protocols.

Collaborating Labs

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

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.


Contact Information

Danielle Swaney

1650 Owens St

Gladstone Institutes

San Francisco, CA, 94158

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Announcements

PROBLEM: observing a loss of signal in the hydrophobic peptides like shown below note Working hypothesis: C18 spin columns might be leaky, and C18 particles can pass through the tip upon centrifugation and end up in your sample. Some of these C18 particles then can end up getting injected into your LC. Because the Vanquish Neo needle seat is a 0.2um filter, these C18 particles get stuck on the needle seat and end up binding peptides from subsequent injections,…
If you have any suggestions for future symposium please let us know.
Postdocs Wanted!
Looking for motivated postdocs to apply proteomics and functional genomics techniques to study Alzheimer's disease. Send your CV to Danielle Swaney if interested.