Mass Spectrometry-Based Global Proteomic Services


Core Director:  Susan Fisher, Ph.D.

Core Director of Operations:  Steven Hall, Ph.D.

Proteomics Instrument

The Proteomics Facility of the Bioassay Core provides EaRTH Center members with global mass spectrometry (MS)-based, protein-level data from in vitro, animal, and human studies. These data enable important insights into biological pathways by which environmental factors exert effects in various experimental models and clinical studies. The available experimental workflows support identification and relative quantification of protein biomarkers and other early indicators of biological perturbations associated with environmental exposures or specific genotypes.

The Proteomics Facility operates under the auspices of the UCSF Sandler-Moore Mass Spectrometry (SMMS) Core Facility, located at Parnassus Heights and has served as a campus core since 2003. The core’s mission is to provide MS tools to the UCSF research community including a variety of scientific instrumentation along with an array of associated bioinformatics hardware and software. In this regard, we are positioned to offer an all-inclusive suite of comparative proteomic MS-based services. They include various approaches to protein identification, quantification, and data interpretation. We also provide consultation with regard to experimental design, sample preparation, data publication and grant writing. In addition, the SMMS Core Facility has a strong commitment to educating its users. Venues that enable this process include seminars and training classes, which keep users abreast of the latest developments in sample preparation, MS technology and instrumental design as well as basic MS theory as it applies to biomacromolecules.

Our central experimental workflow focuses on the identification and quantification of protein biomarkers. For identification, we employ a traditional data-dependent “shotgun” approach. Differential expression/relative quantification of these candidates among samples is determined using the novel data independent acquisition method—Sequential Windowed Acquisition of all THeoretical fragment ion spectra mass spectra (SWATH-MS).



  • Project design consultation
  • Sample preparation consultation
  • In-house sample preparation including enzymatic protein digestion, SDS-PAGE, HPLC peptide separation/fraction collection
  • Multiple Affinity Removal System (MARS) depletion of the 14 most abundant proteins in human blood plasma
  • MS-base protein identification from complex mixtures
  • SWATH-MS for identification and relative quantification of proteins among samples
  • Data interpretation including heat mapping, principle component (PCP), gene ontology (GO), and regression analyses
  • Grant writing consultation
  • Scientific journal publication consultation





UCSF Sandler-Moore Mass Spectrometry Core Facility
513 Parnassus Ave.
Medical Sciences Building S875
San Francisco, CA 94143
[email protected]