Proteomics and Macromolecular Crystallography

Rajesh Soni, Ph.D., Manager, Proteomics
Farhad Forouhar, PhD, Manager, Crystallography

Mass Spectrometry Proteomics

The Proteomics Shared Resource supports both discovery-based and targeted proteomic analysis. The facility provides cancer researchers access to the state-of-the-art mass spectrometers and software for qualitative (e.g. protein identification), quantitative (e.g. relative quantification), and post-translational modification (PTM) analyses. The services include i) mass determination of purified proteins/peptides, ii) identification of purified protein complexes, iii) site-targeted PTM mapping on purified proteins, targeted MRM quantification, iv) global proteome analysis, subproteome isolation and identification, and v) large-scale PTM characterization. The facility director and dedicated technical personnel have extensive expertise in mass spectrometry-based techniques and will provide consultation on experimental design, data analysis, and troubleshooting. We encourage researchers to contact us prior to submission of samples to discuss sample preparation, experimental design, and potential outcomes of research projects.

The Proteomics SR uses the iLab Core Management System for service requests and billing. To schedule equipment and make service requests, go to the iLab web site  and log in with your UNI and password. 

Specific Services Provided

  • Protein Identification (gel band and section)
  • Quantitative proteomics of affinity enriched protein complexes (IP, BioID, APEX2, etc.)
  • Global quantitative proteomics analysis (Label free (LFQ) & Label (SILAC & TMT)
    • Proteome analysis
    • Post-translational modifications (PTM) analysis (phosphorylation, ubiquitination, etc.)
  • Quantitative and targeted proteomics of cell signaling pathways (Immuno-affinity enrichment)
    • (PI3K/AKT, AMPK, PKC, CDK, MAPK, JNK cascades, T-cell and B-cell receptor signaling, etc.)
  • Exosome proteomics profiling
  • Targeted protein/peptide characterization/ quantification (customized PRM)
  • Custom proteomics for innovative projects
  • HICCC PSR Mass Spectrometers

    • Fusion Tribrid Mass Spectrometer + Dionex Ultimate 3000
    • QE HF mass spectrometer + Eksigent nanoLC-Ultra 2D HPLC system
    • UltraflexXtreme MALDI TOF/TOF mass spectrometer


    • Proteome Discoverer & MaxQuant (Database search)
    • Scaffold (Data processing & visualization)
    • Skyline (Targeted proteomics analysis)
    • Perseus (Statistical analysis & data visualization)