# Equipment Supplement Request for a Research Resource for Ultra-sensitive High Throughput Proteomics

> **NIH NIH P41** · BATTELLE PACIFIC NORTHWEST LABORATORIES · 2021 · $233,010

## Abstract

Abstract
Parent grant TR&D 1: The overarching goal of the Resource is to dramatically improve on the existing
proteomics paradigm by achieving orders-of-magnitude gains in both measurement sensitivity and
throughput, as well as to address important measurement ‘blind spots’ and shortcomings of current
methods. At present, a minimum of thousands of cells are generally required for in-depth coverage of
proteins in a biological sample, precluding many important applications involving extremely small
samples, rare cell types or spatially resolved measurements. We have recently developed a Nanodroplet
Processing in One-pot for Trace Samples (NanoPOTS) technology which, when coupled with
ultrasensitive MS-based measurements, enables effective analysis of as few as 10 mammalian cells. The
technology efforts of TR&D 1 will extend this robotic/microfluidic NanoPOTS platform to provide the
‘up-front’ processing required to efficiently handle ultra-small samples (extending to single cells) and
deliver these samples optimally to the Structures for Lossless Ion Manipulations (SLIM)-based ion
mobility-mass spectrometry (IM-MS) platforms to be further advanced under TR&D 2. The robotic
platform will enable samples to be transferred using nanoelectrospray ionization to the SLIM IM-MS
platforms with high ionization and utilization efficiencies. The nanoPOTS platform and workflow will be
optimized to enable broad proteome coverage for sample sizes in the range of 1-1000 cells so as to enable
broad proteome coverage. The efforts will also establish seamless, automated integration of nanoPOTS
with the widely used cell isolation technologies of fluorescence activated cell sorting (FACS) and laser-
capture microdissection (LCM), enabling ultra-rare cell analysis and high-resolution proteome mapping
of clinical tissues. We will also extend NanoPOTS processing to address the inherently small sample
sizes and sensitivity challenges associated with functional proteomics measurements, including activity-
based proteomics and measurements of key post-translational modifications such as phosphorylation,
using a combination of direct surface functionalization, magnetic bead-based workflows within the
nanowells and microcolumn fractionation to enrich and process functional protein subpopulations. We
aim to reduce required sample sizes for such functional measurements by more than 100-fold. The
efficient processing and greatly reduced sample losses enabled by the nanoPOTS platform will
complement the large gains in throughput and sensitivity afforded by TR&D 2 and its fast and high-
resolution gas-phase separations and manipulations in SLIM. The workflows to be developed will enable
both online and offline separations (e.g., liquid chromatography) with SLIM IM-MS using NanoPOTS-
prepared samples. The development of this platform will occur in close collaboration with the TR&D 2
and 3 efforts and is key to most of the driving biological projects.

## Key facts

- **NIH application ID:** 10398678
- **Project number:** 3P41GM103493-19S1
- **Recipient organization:** BATTELLE PACIFIC NORTHWEST LABORATORIES
- **Principal Investigator:** RICHARD D SMITH
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $233,010
- **Award type:** 3
- **Project period:** 2003-09-15 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10398678

## Citation

> US National Institutes of Health, RePORTER application 10398678, Equipment Supplement Request for a Research Resource for Ultra-sensitive High Throughput Proteomics (3P41GM103493-19S1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10398678. Licensed CC0.

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