# MASH Explorer, a Comprehensive Software Environment for Top-Down Proteomics

> **NIH NIH R01** · UNIVERSITY OF WISCONSIN-MADISON · 2021 · $289,363

## Abstract

Project Summary
 In the post-genomic era, proteomics is the next frontier allowing an in-depth understanding of the function
of cellular systems in human diseases and the development of personalized treatments. Unlike the genome, the
proteome is dynamic and highly complex due to alternative splicing and post-translational modifications (PTMs).
The emerging top-down proteomics is the most powerful method to comprehensively characterize proteoforms
that arise from genetic variations and PTMs, which is critical for understanding disease mechanisms and
identifying new therapeutic targets. However, data analysis tools for top-down proteomics remain under-
developed. With the recent rapid growth of the top-down proteomics community, there is an urgent need to
develop a comprehensive analysis platform for top-down proteomics. Herein, we aim to develop MASH Explorer,
a comprehensive, universal, and user-friendly software environment for top-down proteomics, which includes
both an offline downloadable software package (App) and an online version for data processing and analysis
(Portal). The specific aims are: 1) to develop MASH Explorer App, a downloadable software package for top-
down proteomics that can process data from various vendor formats and incorporate multiple algorithms for
deconvolution and database search with user-friendly graphical interfaces; a novel deconvolution algorithm for
high-accuracy data analysis and a novel search algorithm for identification of large proteins will also be
developed to address the deficiency in the currently available top-down proteomcis software tools; 2) to develop
novel algorithms for the automated identification and quantification of proteoform families with enhanced
identification of low-abundance proteoforms; 3) to develop MASH Explorer Portal, a web-based extension of
MASH Explorer App for processing and sharing top-down proteomics data. The MASH Explorer Portal features
my MASH, a cloud-based personalized space for online data processing, as well as MASH public, a public
database for long-term data storage and sharing to facilitate the collaboration among various groups and the
entire proteomics community. The successful completion of this project will create a powerful software tool,
MASH Explorer, for top-down proteomics. The MASH Explorer software will be freely available to all users.
Improving the accessibility of non-proprietary free software solutions will significantly bolster the growth of the
top-down proteomics community. Hence, we envision it will play integral roles in advancing the burgeoning field
of top-down proteomics and realize its full potential for biomedical research.

## Key facts

- **NIH application ID:** 10124406
- **Project number:** 5R01GM125085-04
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** Ying Ge
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $289,363
- **Award type:** 5
- **Project period:** 2018-06-01 → 2023-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10124406

## Citation

> US National Institutes of Health, RePORTER application 10124406, MASH Explorer, a Comprehensive Software Environment for Top-Down Proteomics (5R01GM125085-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10124406. Licensed CC0.

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