University of Rochester Medical Center Proteomics Core

Staff within the PRL provide assistance with project design and planning, proper sample preparation (sample clean-up, protein concentration, western blotting, 1D and 2D gel electrophoresis, affinity-based enrichment, liquid chromatographic separations and proteolytic digestion) and interpretation of mass spectrometric data. Routine analyses involve the identification of unknown proteins, characterization of protein complexes, mapping of post-translational modifications (PTMs) and relative quantification of peptides/proteins/small molecules from a wide range of sample types, including complex clinical matrices, tissue extracts and cell lysates. Specialized MS instrumentation operated and maintained by the PRL include: a ThermoFisher TSQ Quantum Access Max triple quadrupole for small molecule/peptide quantitation assays, a ThermoFisher Orbitrap XL and a LTQ linear ion trap for peptide/protein identification experiments, a Bruker micrOTOF QII quadrupole time-of-flight instrument for small molecule characterization studies, and a Bruker Apex Ultra 9.4T Fourier Transform ion cyclotron resonance mass spectrometer for intact protein mass determination and “top down” proteomics experiments. In addition, the laboratory has access to a variety of automated database searching software (Mascot, SEQUEST, X!Tandem) and PRL staff have the ability to carry out de novo peptide sequencing for discovery-based proteomics projects.