The mission of the USC Proteomics Core is to make the cutting edge mass spectrometry technology available to the entire USC research community. While the core is a fee-for-service facility, it is also a research environment for multi-disciplinary research and education that utilizes mass spectrometry and other proteomics technologies to tackle complex biological and medical problems. It educates and provides support for users to design and tailor proteomics experiments to obtain high quality data for publications (see recent list of recent publications below) and grant proposals. The core also continually innovates on existing technologies.

The Core provides high-sensitivity and high-resolution mass spectrometry for protein and peptide analysis as its primary technology. The Core is a university-wide resource and is supported by funds from the Office of Provost, Keck School of Medicine and Center for Liver and Digestive Diseases. This state of the art facility was established and is headed by Dr. Ebrahim Zandi, associate professor of molecular microbiology and immunology and the faculty director of the Proteomics Core. The core is managed by senior technical expert, Dr. Yu Zhou. Services include protein identification and protein quantitation from a wide variety of sample types from simple mixtures (gel spots and bands) to complex mixtures (protein complexes, cell lysates, and plasma). The Proteomics Core is located in Hoffman Medical building (HMR 511/513) at the Keck School. Recently, a Q Exactive™ Hybrid Quadrupole-Orbitrap Mass Spectrometer and an EASY-nLC 1000 Liquid Chromatograph were added to the core equipment. The core also operates a LTQ Orbitrap XL™ ETD Hybrid Ion Trap-Orbitrap Mass Spectrometer and an Eksigent nanoLC 2D.

Examples of services provided by the core are sample preparation, including digestion of proteins in gel or solution, depletion of the most abundant serum proteins to study the protein differences in patients’ samples, identification of unknown proteins from gel pieces or solutions, characterization of protein post-translational modifications and identification of the modification sites. Commonly identified protein modifications include phosphorylation, deamidation, acetylation, methylation and ubiquitination. The core also provides quantitative protein and peptide analysis using TMT, iTRAQ, SILAC and/or label-free methods and bioinformatic analysis, including protein annotation and protein-protein interaction network analysis. A detail of services provided can be found on the core website: https://keck2.usc.edu/Research/Centers_and_Programs/Proteomics_Core_Facility.aspx.

Selected Recent Publications with contribution from the core:

1. He S, Zhao J, Song S, He X, Minassian A, Zhou Y, Zhang J, Brulois K, Wang Y, Cabo J, Zandi E, Liang C, Jung JU, Zhang X, Feng P. Viral pseudo-enzymes activate RIG-I via deamidation to evade cytokine production. Mol Cell. 2015 Apr 2;58(1):134-46. doi: 10.1016/j.molcel.2015.01.036. Epub 2015 Mar 5.
2. Yang H, Li TW, Zhou Y, Peng H, Liu T, Zandi E, Martínez-Chantar ML, Mato JM, Lu SC., Activation of a Novel c-Myc-miR27-Prohibitin 1 Circuitry in Cholestatic Liver Injury Inhibits Glutathione Synthesis in Mice, Antioxid Redox Signal., 2015, 20;22(3):259-74.
3. Liu Y, Yang R, Liu X, Zhou Y, Qu C, Kikuiri T, Wang S, Zandi E, Du J, Ambudkar IS, Shi S., Hydrogen sulfide maintains mesenchymal stem cell function and bone homeostasis via regulation of Ca(2+) channel sulfhydration, Cell Stem Cell. 2014 , 3;15(1):66-78.
4. Xu S., Butkevich AN, Yamada R., Zhou Y., Debnath B, Duncan R, Zandi E, Petasis NA, Neamati N., Discovery of an orally active small-molecule irreversible inhibitor of protein disulfide isomerase for ovarian cancer treatment., Proc Natl Acad Sci U S A. 2012, 109(40):16348-53.
5. Liu Y., Fang Y., Zhou Y., Zandi E., Lee CL, Joo KI, Wang P. Site-specific modification of adeno-associated viruses via a genetically engineered aldehyde tag., Small. 2013, 9(3):421-9.