Supported by CCR Office of Science and Technology Resources (OSTR)

Protein Characterization Laboratory


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The PCL offers various technologies to CCR investigators for the characterization of proteins and metabolites. The laboratory 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 and metabolite levels. The PCL engages in both short- and long-term collaborations based on the need of each project. The PCL is operated by Leidos Biomedical Research Inc. on behalf of NCI as part of the Frederick National Laboratory.

Established Technologies

Protein and Proteomics Analysis:

The PCL specializes in the identification and characterization of individual proteins, global proteomics analysis from 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.

Protein identification and characterization from different sample types using 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).

Metabolite and Metabolomics Analysis:

The laboratory specializes in identification and quantification of small molecules and metabolites utilizing targeted MRM assays in complex biological samples. Conducts analysis of key cellular metabolite pathway using targeted MRM panel assays. And carries out untargeted metabolomics profiling in variety of biological matrixes.

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.

Analysis of entire metabolic pathways using targeted MRM panel assays covering key pathways involved in the metabolism of cells and cancer.

Over 150 available targeted MRM assays spanning many of the key cellular metabolite pathways such as the glycolysis, pentose phosphate, TCA, oxidative phosphorylation, amino acids and numerus derivatives, nucleotides (purine and pyrimidine) and short- medium and long chain fatty acids.

Identification and quantitation of steroid hormones (estrogen, progesterone and androgen) in different biological matrixes

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

Global untargeted metabolomics analysis. Samples are analyzed under two different LC conditions using Reverser Phase chromatography (RP) and Hydrophilic interaction chromatography (HILIC) ran under two different pH conditons (pH3 and pH9), in both negative and positive ionization mode. Spiked in isotopic standards, water blanks, pool samples and reference samples are used for data filtration, normalization, and QC assessment.

Emerging Technologies

Spatial Proteomics



*All coupled to nano flow liquid chromatography HPLCs.

Orbitrap Eclipse mass spectrometer

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Orbitrap Fusion Tribrid mass spectrometer

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Q Exactive HF

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*All coupled to high flow HPLCs.

Orbitrap Q Exactive Mass Spectrometers

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TSQ Quantiva Mass Spectrometer

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TSQ Altis Mass Spectrometer

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Our Team

Thorkell Andresson, Ph.D.

Facility Head

Phone: 301-846-7190
Cell: 240-840-1383