# Novel Technologies for Protein Analysis

> **NIH NIH R35** · UNIVERSITY OF WISCONSIN-MADISON · 2020 · $250,000

## Abstract

PROJECT SUMMARY
This proposal is for an equipment supplement to our MIRA to purchase a Fusion Lumos mass spectrometer.
The goals of the overall MIRA remain the same and its original summary statement is provided below.
The primary focus of our laboratory is the development of novel technologies for protein analyses, specifically
centered around the concept of the proteoform. Proteoforms, each of which comprises a unique combination of
amino acid sequence and post-translational modifications (PTMs), are the primary molecular effectors of cell
function. Subtle sequence and PTM differences between proteoforms can completely alter their function and
activity. We see comprehensive proteoform-level analysis of biological systems as absolutely essential to
understanding their function, for both individual pathways and networks operative within cells, and more
globally, to decipher the systems-biology-level dynamics and interactions that control cellular response.
However, today’s technology for global proteoform analysis in complex systems is in its infancy, offering both a
great challenge and a great opportunity. We seek to develop novel strategies for comprehensive proteoform
identification and quantification in complex systems. We envision combining information from multiple data
streams, such as transcriptomic data (to reveal splice forms and genetic variation), bottom-up proteomics data
(to reveal and localize PTMs), top-down proteomics data (to provide sequence tags for proteoform
identifications), and intact mass measurements (to identify and quantify proteoforms, using information from all
of the other data streams). Specific projects will develop the following: (1) robust tools for the construction of
sample-specific proteoform databases; (2) new strategies for the discovery and localization of PTMs; (3)
improved sample preparation, separation, and mass spectrometry methods for intact proteins; (4) synergistic
approaches that utilize both intact mass measurements and selected top-down fragmentations to maximize
proteoform identifications; and (5) visualization tools for proteoform families that show connections and
changes between related proteoforms. We will integrate these methods and data streams together with
powerful open-source software and accompanying protocols to make these capabilities widely available,
enabling researchers everywhere to gain a deeper understanding of the functioning of their biological systems.
We will apply our innovative tools to many cutting-edge projects with numerous collaborators, both because
technology development is most meaningful in the context of relevant biological studies and because it will
increase the adoption of proteoform analysis among scientists in the broader biomedical community.

## Key facts

- **NIH application ID:** 10134007
- **Project number:** 3R35GM126914-03S1
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** LLOYD M SMITH
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $250,000
- **Award type:** 3
- **Project period:** 2018-05-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10134007

## Citation

> US National Institutes of Health, RePORTER application 10134007, Novel Technologies for Protein Analysis (3R35GM126914-03S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10134007. Licensed CC0.

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