# Proteostasis Core: Quantitative global proteomics

> **NIH NIH P01** · NORTHWESTERN UNIVERSITY · 2020 · $216,923

## Abstract

Project Summary / Abstract (Core C)
Core C will conduct global proteomics experiments for project participants. This work will be performed under
the leadership of Drs. Steve Gygi and Daniel Finley at Harvard Medical School (HMS). The renowned facility at
HMS can provide quantitative readouts of protein levels of 10 samples at once, using the TMT-MS3 method of
global proteomics developed by the Gygi group. A single run of 10 samples provides detailed quantitative data
on 10 experimental proteomes. This comprehensive view of perturbations under defined experimental
conditions yield a wealth of information, including the levels of over 1000 components of the proteostasis
network (PN), such as proteasomes and chaperones, the state of thousands of substrates of these enzymes,
and the occupancy of ~30,000 protein modification sites. Importantly, each TMT-MS3 run will provide a
fingerprint of the state of the PN at a given time and condition. Thus, the phenotypic characterization of new
mutants in the PN, such as transgenic mutants with enhanced proteasome activity, will be accomplished at the
highest resolution possible at present. Core C will also give researchers access to a second proteomics
signature: a global account of ubiquitin modifications of proteins. This will be accomplished using the “GG
pulldown” method, in which tryptic peptides bearing diglycine remnants from ubiquitin are enriched via
immunopurification prior to mass spectrometry. TMT proteomics and ubiquitin proteomics, applied in parallel,
will provide a uniquely detailed and informative snapshot of the state of the PN in a cell. These analytical
approaches will be invaluable to all projects within the team, including core projects that focus on biosensors
(Core B) and chemical regulators of the PN (Core D). In addition, proteomics approaches of the proteasome
and autophagy projects (2 and 3), involving in vivo work in the mouse, will be closely coordinated so that the
resulting datasets can be integrated and subjected to metadata analysis. Thus, the methodologies of Core C
will help to unite the research efforts of the project and to drive our understanding of PNs to a more quantitative
and systematic level.

## Key facts

- **NIH application ID:** 9962253
- **Project number:** 5P01AG054407-03
- **Recipient organization:** NORTHWESTERN UNIVERSITY
- **Principal Investigator:** Daniel J Finley
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $216,923
- **Award type:** 5
- **Project period:** — → —

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9962253

## Citation

> US National Institutes of Health, RePORTER application 9962253, Proteostasis Core: Quantitative global proteomics (5P01AG054407-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9962253. Licensed CC0.

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