The Children’s Hospital of Philadelphia Research Institute (CHOP) Proteomics Core Facility (PCF) provides a variety of protein and proteomics services for investigators at CHOP, University of Pennsylvania, and outside institutions. These services include producing and characterizing proteins, investigating protein-protein interactions, and characterizing whole proteomes. Some services are provided on a user-operated, sign-up basis, while others are performed as full-service by the dedicated facility personnel. Protein expression services include recombinant protein production in bacteria. HPLC and FPLC equipment, columns and resins are available for a variety of purification needs. Endogenous fluorescence, circular dichroism, and analytical ultracentrifugation can be used to characterize folding status of proteins and their interactions with small molecules and other proteins or nucleic acids.
A wide range of state-of-the-art proteomics experiments are possible. These include, but are not limited, to intact mass determination, post-translational modification analysis, protein identification, and targeted (e.g. co-immunoprecipitation) or comprehensive (e.g. protein expression profiling) proteome analysis. Proteome analysis may employ a number of different isotope-labeling strategies enabling quantitative measurements on our high resolution discovery platforms (Orbitrap-Elite and Q-Exactive HF mass spectrometers) for deep proteome coverage or multiplexed targeted quantification on our triple quadrupole mass spectrometer (Xevo-TQS). Unique among regional cores is our ability to quantitatively analyze proteomes, phosphoproteomes, ubiquitylomes, and lysine acetylomes at a deep level through a process of serial enrichment. Under development are refinements of statistical and bioinformatic analyses of proteomic results. It is also possible to tailor sensitive and specific methods for multiplexed protein quantification according to the investigator’s needs. Workflows for all the aforementioned protein and proteome analyses are unique to each project and can involve a range of multi-dimensional separation techniques coupled to the appropriate mass spectrometer. For all but the most routine services and/or first-time submissions, a strong interaction with PCF staff and consultation with Dr. Seeholzer is encouraged throughout all phases of a project: planning, execution, and data reduction/interpretation.