# An ultrasensitive targeted mass spectrometry system for proteomics analysis of single cells

> **NIH NIH R21** · BATTELLE PACIFIC NORTHWEST LABORATORIES · 2020 · $171,393

## Abstract

ABSTRACT
Cancer is a heterogeneous disease originating from an accumulation of genetic and epigenetic mutations in a
single normal cell. Precise characterization of a broad spectrum of heterogeneous populations of tumor cells
within individual patients at different molecular levels would greatly facilitate understanding of tumor
initiation, progression, metastasis and therapeutic response with the potential to move toward precision
medicine. With recent advances in antibody-based flow cytometry and mass cytometry, high-throughput
targeted proteomics analysis of single cells has become possible. However, they share common shortcomings
with other antibody-based methods, and lack quantitation accuracy to provide absolute protein amounts or
concentrations. Mass spectrometry (MS)-based targeted proteomics has emerged as an alternative in terms of
its being antibody-free, high multiplex, and high precision/accuracy. However, there are two major technical
challenges for targeted MS analysis of single cells: 1) effective processing of single cells, and 2) sufficient MS
sensitivity. To address these two challenges, we propose to develop an ultrasensitive targeted MS system for
enabling rapid, comprehensive, precise analysis of single cells. The new development is built upon
1) incorporation of a new `carrier protein' concept into our simplified nano-proteomics preparation platform
(SNaPP) for automated robust processing of single cells, and 2) leveraging disruptive MS technologies
pioneered at Pacific Northwest National Laboratory with effective integration of high-efficiency SPIN (sub-
ambient pressure ionization with nanoelectrospray) source and ultrafast high-resolution SLIM (structures for
lossless ion manipulation)-based ion mobility separation with a state-of-the-art high resolution/ sensitivity
time-of-flight (TOF) MS through electrodynamic ion funnel interfaces for high-efficiency ion transmission.
When coupling with ultralow-flow high-resolution reversed-phase liquid chromatography (LC), the new MS
platform is expected to provide >50 and ~100-fold improvement in sensitivity and sample throughput,
respectively (i.e., ~0.2-2 zmols or ~120-1200 molecules of sensitivity and ~5-10 mins per sample) when
compared to standard targeted MS platforms. In combination with cSNaPP for effective processing of single
cells, such levels of improvement could allow the new LC-MS platform for precise quantification of the majority
of the entire proteome in single cells and ~150 samples per day. We anticipate that the new MS system will
become a convenient indispensable quantitation tool for routine proteomics analysis of single cells and make
substantial contributions to current biomedical research.

## Key facts

- **NIH application ID:** 9960303
- **Project number:** 5R21CA223715-03
- **Recipient organization:** BATTELLE PACIFIC NORTHWEST LABORATORIES
- **Principal Investigator:** Tujin Shi
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $171,393
- **Award type:** 5
- **Project period:** 2018-07-15 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9960303

## Citation

> US National Institutes of Health, RePORTER application 9960303, An ultrasensitive targeted mass spectrometry system for proteomics analysis of single cells (5R21CA223715-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9960303. Licensed CC0.

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