# Structure, Function and Regulation of the Proteome

> **NIH NIH R35** · UNIVERSITY OF WISCONSIN-MADISON · 2022 · $877,754

## Abstract

PROJECT SUMMARY
My laboratory innovates mass spectrometry (MS) technology to accelerate the pace, depth, and accuracy of
proteome analysis and applies these technologies to globally access proteome structure, function, and
regulation. Signature achievements include the development of electron-transfer dissociation (ETD), the GC-
Orbitrap mass spectrometer, novel protein quantification technologies, and the targeted technique parallel
reaction monitoring – to name a few. Having established our reputation in proteomics instrumentation, our
mission came to include the investigation of the metabolome and lipidome. The rationale is simple: fully
understanding a biological system requires knowing the interplay between molecular classes. We have
demonstrated the capability of these technologies to propel numerous projects in the fields of metabolism,
developmental, and systems biology.
Building on my program’s expertise in the analysis of disassembled molecular machinery (i.e., shotgun
proteomics), we have turned our attention to the machine as a whole, i.e., protein structure. By combining
technologies from MS and cryogenic electron microscopy (cryo-EM) our aim is to maximize the information
garnered from a single sample to provide insight into protein structure with unprecedented speed and simplicity.
That is, we compound the orthogonal information offered by MS measurements of chemical makeup with atomic-
level information afforded by cryo-EM imaging. Further, drawing on concepts from astrophysics already resonant
with MS, we anticipate that our highly creative method will overcome pervasive bottlenecks in cryo-EM sample
preparation that often limit image resolution. To that end, we have adapted a mass spectrometer to purify and
land native protein complexes on cryogenically cooled TEM grids, which are then coated with amorphous ice in
vacuo. The resulting grid would represent the ideal cryo-EM sample – a high density of particles situated in
random orientations in the same focal plane and covered with only a few nanometers of ice. We plan to achieve
even greater structural insight through the incorporation of gas-phase dissociation techniques, which partition
the macromolecule into its subcomponents. In particular we propose the addition of surface-induced dissociation
(SID) and activated-ion ETD (AI-ETD) to the mass spectrometer used for grid preparation. In short, this
technology has genuine potential to create a new paradigm of proteome-scale structural biology.

## Key facts

- **NIH application ID:** 10401900
- **Project number:** 5R35GM118110-07
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** Joshua J Coon
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $877,754
- **Award type:** 5
- **Project period:** 2016-05-05 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10401900

## Citation

> US National Institutes of Health, RePORTER application 10401900, Structure, Function and Regulation of the Proteome (5R35GM118110-07). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10401900. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*