Protein and Proteomics Core


The 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. The PCF provides some services on a user-operated, sign-up basis, while dedicated facility personnel perform others as full-service.

Unique among regional cores is the PCF’s 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.

Protein expression services include recombinant protein production in bacteria. High-performance liquid chromatography and fast protein liquid chromatography 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
  • Targeted (e.g. co-immunoprecipitation) or comprehensive (e.g. protein expression profiling) proteome analysis.

Proteome analysis may employ various 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).

Workflows for all the aforementioned protein and proteome analyses are unique to each project and can involve a range of multidimensional 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 the director is encouraged throughout all phases of a project: planning, execution, and data reduction/interpretation.