CCR Protein and Metabolite Characterization Core (PMCC)

Protein and Metabolite Characterization Core offers various technologies to CCR investigators to characterize proteins and metabolites. The core develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, and liquid chromatography, to advance the understanding of cellular function at the protein, proteomics, metabolite, and metabolomic levels. It engages in both short and long-term collaborations based on the need of each project. It is operated by Leidos Biomedical Research Inc. on behalf of NCI as part of the Frederick National Laboratory.

Expertise and Technology

• Protein identification and characterization from different sample types using a variety of proteases, separation, and mass spectrometry methods.
• Characterization of complex proteomes (e.g., serum, tissue, cell lysates)
• Global comparative proteomic quantitation using TMT, SILAC, dimethyl labeling and/or LFQ
• Identification and characterization of protein modifications – PTM site mapping
• Global comparative Posttranslational Modification (PTM) quantitation using TMT, SILAC, dimethyl labeling, LFQ and affinity enrichment for modifications such as phosphorylation, ubiquitination, and acetylation
• MHC I and II peptide identification and global immunopeptidome analysis.
• Protein complex isolation and characterization
• Validation of protein-protein interaction
• Identification of protein-nucleic acid (DNA, RNA) interaction
• Protein contact mapping using mass spectrometry cleavable cross linkers
• Intact protein analysis, protein-drug conjugate analysis
• Analytical protein and peptide fractionation using different methods such as size exclusion chromatography (SEC), reverse phase (RP) and ion exchange (SCX).
• Relative and absolute quantification of metabolites using MRM based targeted assay incorporating isotopic standards for increased identification and quantification accuracy
• Develops and establishes custom targeted metabolite assays for small molecules and metabolites.
• Identification and quantification of modified nucleotides (DNA and RNA).
• Pharmacokinetics (PK) analysis, develop quantitative MRM assay for known and novel drugs and small molecules. Analyzing drug metabolites in relevant biofluids and tissues.
• Purity determination and structural analysis of small molecules
• Isotope tracing to monitor metabolite pathway activities

Protein and proteomics analysis:

The core specializes in the identification and characterization of individual proteins, global proteomics analysis from a variety of different starting materials, targeted and global analysis of macromolecular post-translational modifications, characterization of entire protein complexes and other macromolecular interactions, protein cross-linking mapping, and intact protein mass analysis.

Metabolite and metabolomics analysis:

The core specializes in assay development for the identification and quantification of small molecules and metabolites utilizing targeted MRM assays in complex biological samples. For projects requiring 'Routine' metabolomics support, please visit the NIH Metabolomics Consortium (NIH-MC).