The Nanoscale Protein Analysis Section of the CCR Collaborative Protein Technology Resource (CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery and translation/clinical studies. Applications include:

  • Quantitative profiling of cell signaling and post-translational modification
  • Measurement of cytokine, metabolite and serum/plasma markers
  • Identification and validation of biomarkers & therapeutic targets
  • Assessment of on‐ and off‐target drug activity and pharmacodynamic evaluation
  • Study of tumor microenvironment and single-cell signaling

Established Technologies

Automated capillary immunoassay system – Simple Western technology

  • High-resolution MW (size-based) or isoelectric-focusing (IEF, charge-based) separation, followed by target-specific immunoprobing to profile proteins and respective post-translational modification isoforms
  • Nanogram level of protein analysis for extremely small and precious samples, e.g. stem cells, primary cells, micro-dissected samples, fine needle aspirates, non- or minimally- invasive collected patient specimens etc.
  • Provides precise and accurate measurement of protein expression level and activation status, highly quantitative data, good assay sensitivity, dynamic range and reproducibility
  • About three hundred assays covering key signaling pathways have been established and successfully applied for functional proteomic research, will validate assays for other targets as needed
  • Assay readiness for bench to bed transfer

In-solution multiplex ELISA assays – Luminex xMAP Technology

  • Up to 50-plex simultaneous protein target analysis with small sample consumption
  • Analysis of cytokine, metabolite, immune response, serum/plasma biomarkers etc.
  • Clinical applicable assay performance

Immunofluorescence imaging platform – CODEX (CO-Detection by indEXing) technology

  • Provides full spatial context and is not limited to just regions of interest (ROI)
  • Provides single-cell resolution down to 600 nm or 250 nm depending on microscope objective used (20X and 40X respectively)
  • Single-step staining and gentle fluorophore removal preserves the sample for ROI analysis
  • Simple, benchtop fluidics system that is cost-effective and simple to implement in any research lab

Developing Technologies

Single-cell Western system

  • Western-based protein analysis on 1000-2000 single-cells in parallel
  • Measures proteins hard-to-detect by FACS, such as isoforms, phosphorylated proteins, transcription factors, intracellular proteins etc.
  • Single cell signaling profiling and population heterogeneity study

We actively evaluate, develop, acquire and implement innovative protein analysis technologies to accommodate the demands from the CCR/NCI/NIH community.

Digital Spatial Profiling

  • NanoString GeoMx Digital Spatial Profiling (GeoMx DSP)
  • Offered in collaboration with the CCR Genomics Core
  • FFPE or fresh frozen
  • Profiling data for 100s of validated proteins
  • Cancer Trascriptome Atlas (CTA) > 1,800 gene
  • Whole Transcriptome Atlas (WTA) > 18,000 genes

User Guidelines

  • Projects are collaborative and subject to the approval of resource advisory committee.
  • Investigators are expected to share the cost of certain consumable reagents, for which CCR investigators are eligible for a 50% subsidy from the CCR Office of Science and Technology Resource (OSTR).
  • Staff are available to assist on project design, data interpretation and study milestone evaluation, as well as general consultation on proteomic analysis questions.


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Contact Information
Noemi Kedei, MD
Facility Head
Building 41, Room D310
Bethesda, MD 20892
Additional Core Staff
Maria O. Hernandez, PhD
Xiaoling Luo