Proteomics and Macromolecular Crystallography Shared Resource (HICCC)

The Proteomics and Macromolecular Crystallography Shared Resource (PMCSR), managed by the Herbert Irving Comprehensive Cancer Center, provides access to advanced proteomic technologies and structural information of macromolecules (i.e. protein, DNA, RNA) at the atomic resolution for CUIMC researchers. PMCSR services include: (1) protein identification (gel band and section), (2) quantitative proteomics of affinity enriched protein complexes (IP, BioID and APEX2), (3) global quantitative proteomics analysis (label-free [LFQ] & labeled [SILAC & TMT]), (4) quantitative and targeted proteomics of cell signaling pathways (immuno-affinity enrichment), (5) exosome proteomics profiling, (6) targeted protein/peptide characterization/quantification (customized PRM), (7) structural modeling of proteins, and (8) determination of protein crystal structures, at atomic resolution in an apo form and in complex with natural ligands or inhibitors, and in complex with other macromolecules. Consulting services in experimental design are conducted by expert personnel in the PMCSR who facilitate the incorporation of advanced techniques into the research portfolio of CUIMC investigators. The PMCSR is located in the Lasker Biomedical Research Building.

Equipment

  • Thermo Scientific Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer
  • Thermo Scientific Orbitrap Fusion Tribrid Mass Spectrometer
  • UltrafleXtreme MALDI-TOF
     

Software

  • MaxQuant
  • Perseus
  • Proteome Discoverer 2.2
  • Scaffold 4.0 
  • Spectronaut Pulsar X (Biogenosys)
  • Skyline
  • Ingenuity Pathway Analysis (IPA)
     

The Proteomics and Macromolecular Crystallography Shared Resource (PMCSR) of the Herbert Irving Comprehensive Cancer Center (HICCC) provides access to two high-resolution mass spectrometers, Thermo Scientific Orbitrap Fusion Tribrid, Q Exactive HF hybrid quadrupole-Orbitrap and UltrafleXtreme MALDI-TOF with state-of-the-art capabilities supporting quantitative and functional proteomic analyses. The shared resource has a robust data analysis pipeline for quantitative and targeted proteomics with proprietary proteomic software (Proteome Discoverer 2.2, Scaffold 4.0 and Spectronaut Pulsar X [Biogenosys]). In addition, the shared resource supports crystallographic services for structure elucidation of protein, protein-protein and protein-nucleic acid complexes.

Standards, Rigor, and Reproducibility

Quality control procedures recommended by the instrument manufacturer are in place to ensure proper instrument operation. To ensure rigor and reproducibility, all analytical services include standard operating protocols and are routinely validated using technical replicas.