Cancer Institute A national cancer institute
designated cancer center

Proteomics Shared Resource

Faculty Director: Allis Chien, PhD
Faculty Advisors: Tom Wandless, PhD, Russ Altman, MD PhD, Matt Bogyo, PhD, Steve Boxer, PhD, John Brauman, PhD, Michael Cleary, MD, Josh Elias, PhD, Curt Frank, PhD, Richard Luthy, PhD, Daria Mochly-Rosen, PhD, Mike Snyder, PhD


Allis Chien, PhD
Director, Proteomics Shared Resource
Seely G. Mudd Building, Rm 175 (lab), Rm 167 (office)
Stanford, CA 94305-5080
(650) 723-0710
Fax: (650) 725-0259


The Stanford Proteomic Shared Resource provides state-of-the-art, user-friendly facilities and service in addition to education, methods development and new applications development designed to meet the rapidly evolving needs of Cancer Center investigators. Services include peptide and protein identification, characterization of post-translational modifications, protein quantitation, biomarker verification and metabolic studies.

These analyses extend from the identification of protein complexes purified from in vitro systems, to the characterization of proteins in mouse tissues in transgenic models, to the quantitation of chemopreventive agents and metabolites in human serum. The shared resource has been servicing the research community since the year 2000; services are used by over 100 research labs across campus annually, as well as institutions worldwide. Facility scientists have recognized expertise in proteomics and mass spectrometry, and are committed to helping develop and implement proteomic tools for future diagnostics and clinical tests.


Analytical mass spectrometry services are categorized below. Custom projects falling outside these categories are also welcome; examples include protein folding and non-covalent interaction projects. In addition to services provided by facility staff, an open-access laboratory offering LC-MS, GC-MS and data analysis capabilities is available to trained users 24 hours a day, seven days a week. Please see the facility website for more information.



Quantitative Applications and Assays

General MS Analysis


Since each approach requires customization based on the sample type and the goals of the investigators, the facility provides individualized consultation services, for experimental design and sample preparation as well as data analysis and interpretation.

Informatics Support

Following MS analysis, proteomic data is analyzed using a number of software programs hosted on in-house servers, including Mascot (Matrix Science, UK), Sequest (Thermo Scientific, USA), and Scaffold (Proteome Software, USA).  Mascot results can be viewed interactively through a web browser from on-campus computers.  Sequest results can be imported into Scaffold.  Scaffold combines Mascot, Sequest, and X! Tandem search results and generates an easy-to-interpret result file which can be explored using a free viewer.   Data generated from experiments are archived, and raw data can also be provided for users with alternative analysis capabilities.


One mission of the facility is to educate and empower end users. Individual assistance is provided in planning experiments, as well as with analyzing and understanding the results.  An annual mass spec users’ meeting showcases applications of mass spec across campus and facilitates interdisciplinary interactions.  


The Proteomics Shared Resource is located on the third floor of the Keck Science ground floor of the Seely G. Mudd Building. The main lab entrance, Keck 328 Mudd 175, faces the bamboo grove and Lokey Chem-Bio building, and is unlocked between 8 am and 5pm, Monday through Friday; outside these hours, please enter through Keck 316 authorized personnel may enter through Mudd 175A. Instrumentation is operational 24 hours a day as experiments require.


A website orients new users to the services offered and procedures for accessing the shared resource.  Initial consultation for new projects is highly recommended, and can be arranged by phone, email, or direct walk-in.  After MS analysis, results are typically provided in electronic format which are accessible from researchers’ desktops, either through a web browser or free viewer.  Assistance with data interpretation is considered to be an essential part of any project.  

Training on the open-access instrumentation is provided by appointment.

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