# Novel Technologies for Protein Analysis

> **NIH NIH R35** · UNIVERSITY OF WISCONSIN-MADISON · 2022 · $618,109

## Abstract

Abstract
The primary focus of my laboratory is the development of novel technologies for protein analysis, 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. For
example, one of our projects is to elucidate the interactome between specific nucleic acid sequences and the
proteoforms bound to those DNA or RNA molecules. 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:** 10378644
- **Project number:** 5R35GM126914-05
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** LLOYD M SMITH
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $618,109
- **Award type:** 5
- **Project period:** 2018-05-01 → 2023-09-24

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10378644

## Citation

> US National Institutes of Health, RePORTER application 10378644, Novel Technologies for Protein Analysis (5R35GM126914-05). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10378644. Licensed CC0.

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