# TR&D 7: Cell Specific Proteomics

> **NIH NIH P41** · NORTHWESTERN UNIVERSITY · 2020 · $248,963

## Abstract

Technology Research & Development Project 7: Cell Specific Proteomics
Abstract
One of the primary challenges of quantitative proteomics is the dilution of signal due to sampling. Therefore, in
this TR&D, we seek to create and refine three workflows to sample 10,000-100,000 cells of specific types prior
to proteoform-resolved analysis via top-down proteomics (TDP). We outline a plan of attack involving three
common varieties of clinical samples, namely peripheral blood mononuclear cells (PBMCs) (DBP 5), brain
sections (DBP 10, 12, and 13), diseased tissue (DBP 12 and 14) and solid tumors (DBP 9). We propose three
main strategies to achieve cell specificity and spatial localization, range from actively deployable fluorescence-
activated cell sorting (FACS), to the more venerable method of laser capture microdissection (LCM), to a novel,
more direct method, which employs a picosecond infrared laser (PIRL) to ablate intact proteins prior to top-down
proteomics. We will subsequently analyze collected cell-specific samples by our quantitative TDP platform in
both discovery and targeted modes, with the latter utilizing proteoform-specific assays already developed (like
for KRAS proteoforms in DBP 9) or the many more to emerge from TR&D 6 throughout the proposed granting
period. A specific example derives from our work with PBMCs in DBP 5 (kidney and liver transplant patients),
where a panel of 30 proteoforms has emerged from discovery work. From these candidates, we now need
determine which immune cells are most responsible for this signal through cell type-resolved sampling.
The resulting proteoform-resolved measurements will provide more precise, context-rich, and therefore valuable
data revealing how proteins operate in human disease. Although cell-specific TDP technology does not presently
exist, its development will unlock significant bottlenecks in protein-level science by sharply improved information
about molecular signatures in a proteoform- and cell-specific fashion. While several DBPs will benefit from the
sampling of specific cells and tissue regions prior to TDP by FACS, LCM, and PIRL, these technologies are
applicable to the spatial sampling of proteins within a wide variety of biological contexts, which will directly benefit
a broad range of studies in basic biological, translational and clinical research. The measurement capabilities
will also augment the national infrastructure in proteomics, helping to keep pace with an increasingly competitive
international landscape in science and technology.

## Key facts

- **NIH application ID:** 9854767
- **Project number:** 2P41GM108569-06
- **Recipient organization:** NORTHWESTERN UNIVERSITY
- **Principal Investigator:** NEIL L KELLEHER
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $248,963
- **Award type:** 2
- **Project period:** — → —

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9854767

## Citation

> US National Institutes of Health, RePORTER application 9854767, TR&D 7: Cell Specific Proteomics (2P41GM108569-06). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9854767. Licensed CC0.

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