Scripps Research Logo

Center for Physiological Proteomics


The Center for Physiological Proteomics (CPP) is a high-end mass spectrometry (MS) center located on The Scripps Research Institute's La Jolla campus. Established in 2008, the CPP is dedicated to engaging in sophisticated proteomics collaborations with biological researchers both within and outside of The Scripps Research Institute, offering a valuable resource for research groups interested in proteomics, but lacking the in-house equipment or expertise to perform these experiments independently.

Research Mission

The annotation of enzymatic pathways and signaling networks underlying all patho/physiological processes represents an enormous challenge for researchers in the post-genomic era and an essential step for identification of therapeutic targets for treatment of human disease.

"To really understand biological processes, we need to understand how proteins function in and around cells since they are the functioning units." -Dr. Yates

"Understanding the proteome, the structure and function of each protein and the complexities of protein-protein interactions will be critical for developing the most effective diagnostic techniques at early stages to stop disease in its tracks, and treat disease in the future..." -Dr. Cravatt

The CPP was established to create a unique enterprise for high-end proteomics collaborations with investigators both within TSRI and at other research institutes and universities around the world. These interactions can extend beyond performing proteomics experiments for external collaborators to include the training of interested researchers in state-of-the-art MS-based proteomic methods.

Center Organization

The CPP is directed by Dr. John Yates and co-directed by Dr. Benjamin Cravatt. Dr. Yates is a world-renowned leader in the field of proteomics, where his group has pioneered numerous transforming technologies, including Multidimensional Protein Identification Technology (MudPIT) for shotgun proteomics, the SEQUEST and DTASelect search and data analysis algorithms, and the Stable Isotope Labeling of Amino Acids in Mammals (SILAM) method for quantitative proteomics in mammals. Dr. Cravatt is a leader in the field of functional proteomics, with research aimed at elucidating the roles that mammalian enzymes play in critical physiological and pathological processes, including cancer progression, neurotransmission, and drug abuse/addiction. His research group has developed multiple cutting-edge proteomics technologies including activity-based protein profiling (ABPP), competitive ABPP for inhibitor discovery and development, and the Protein Topography and Migration Analysis Platform (PROTOMAP) for identification of proteolytic cleavage events.

The CPP is staffed by multiple Ph.D.-level scientists and technicians with extensive experience in all aspects of MS-based proteomics, including experimental design, sample preparation, and data analysis and interpretation.


The 2000 square-foot facility houses multiple state-of-the art mass spectrometers (LTQs, an LTQ-Orbitrap ETD, and Triple Quadrupole instruments) and complete lab facilities for cell culture, synthetic chemistry, and sample preparation. The CPP also has computational infrastructure available for MS data analysis.


John Yates III, Ph. D.

Tel: (858) 784-8863
Lab website


Benjamin Cravatt, Ph. D.

Tel: (858) 784-8633
Lab website

Photo of Center for Physiological Proteomics

Selected Publications

Kaschani, Farnusch; Gu, Christian; Niessen, Sherry; Hoover, Heather; Cravatt, Benjamin F, and Van der Hoorn, Renier A. L. (2009) Diversity of Serine Hydrolase Activities of Unchallenged and Botrytis-infected Arabidopsis thaliana. Mol Cell Proteomics. 2009 May8; pp1082-93.

Jordan L. Meier, Sherry Niessen, Heather S. Hoover, Timothy L. Foley, Benjamin F. Cravatt, and Michael D. Burkart. (2009) An Orthogonal Active Site Identification System (OASIS) for Proteomic Profiling of Natural Product Biosynthesis. ACS Chem. Biol., 2009 September29; pp 948-957

Daniel K. Nomura, Jonathan Z. Long, Sherry Niessen, Heather S. Hoover, Shu-Wing Ng and Benjamin F. Cravatt. (2010) Monoacylglycerol Lipase Regulates a Fatty Acid Network that Promotes Cancer Pathogenesis. Cell, 2010 January 8; pp49-61,

Andrew J. Holland, Weijie Lan, Sherry Niessen, Heather Hoover and Don W. Cleveland. (2010) Polo-like kinase 4 kinase activity limits centrosome overduplication by autoregulating its own stability. J.Biol.Chem., 2010 January 25; vol. 188no. pp2191-2198

David J. Shields, Sherry Niessen, Eric A. Murphy, Ainhoa Mielgo, Jay S. Desgrosellier, Steven K. M. Lau, Leo A. Barnes, Jacqueline Lesperance, Michael Bouvet, David Tarin, Benjamin F. Cravatt, and David A. Cheresh. (2010) RBBP9: A tumor-associated serine hydrolase activity required for pancreatic neoplasia. PNAS 2010 February 2; pp2189-2194

Contact Information

The CPP is located in SP3030, Room 3030. Click here for a map.

Tel (858)784-8252 (office)
Tel (858)784-8253 (lab)

Molecular Medicine Seminar Series
Center for Physiological Proteomics
Department Contacts

CA Faculty

Asahara, Hiroshi
Balch, William E.
Boddy, Michael
Buxbaum, Joel
Catz, Sergio
Conti, Bruno
Cravatt, Benjamin
D'Lima, Darryl
DerMardirossian, Celine
Deryugina, Elena
Elias, Darlene
Encalada, Sandra
Felding, Brunhilde
Fowler, Velia
Friedlander, Martin
Gerace, Larry
Gottesfeld, Joel
Griffin, John
Hanneken, Anne
Heeb, Mary Jo
Henderson, Scott
Hoch, James
Johnson, Eric
Kanaji, Taisuke
Koziol, James
Lamia, Katja
Lazzerini Denchi, Eros
Lipton, Stuart
Loring, Jeanne F.
Loskutoff, David
Lotz, Martin
Makarenkova, Helen P.
Mc Millan, Robert
Miles, Lindsey
Milner, Richard
Modena, Brian
Mosnier, Laurent
Paulson, James C.
Perego, Marta
Petrascheck, Michael
Pollard, Kenneth Michael
Quigley, James P.
Reed, Steven
Roberts, Edward
Rosen, Hugh
Ruggeri, Zaverio
Russell, Paul
Saez, Enrique
Smider, Vaughn
Srinivasan, Supriya
Steinhubl, Steven
Sutcliffe, J.
Tan, Eng
Topol, Eric
Vanderklish, Peter
Vogt, Peter K.
Wiseman, Luke
Wittenberg, Curt
Wolan, Dennis W.
Wu, Peng
Wu, Xiaohua
Yang, Xiang-Lei
Yates III, John

FL Faculty

Bannister, Thomas
Bohn, Laura M.
Cameron, Michael
Duckett, Derek
Gill, Matt
Griffin, Patrick
Hansen, Scott
Joazeiro, Claudio
Kamenecka, Theodore
Kissil, Joseph
Luo, Junli
McDonald, Patricia
Miller, Courtney
Niedernhofer, Laura
Phinney, Donald G.
Robbins, Paul
Scampavia, Louis
Schimmel, Paul
Smith, Roy
Spicer, Timothy

Affiliated Faculty

Cline, Hollis
Kojetin, Douglas
Lairson, Luke
Paegel, Brian
Rumbaugh, Gavin
Shen, Ben
Solt, Laura A
Su, Andrew
Wu, Chunlei
Ye, Li

Adjunct Faculty