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Updated: Feb 17, 2026

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Anthony J Cesnik¹, Michael R Shortreed¹, Leah V Schaffer¹

¹Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.

Journal of Proteome Research

|December 3, 2017

Summary

This summary is machine-generated.

Proteoform Suite is a new open-source tool for identifying and quantifying proteoforms. It analyzes proteoform variations and functions, revealing changes in yeast during salt stress.

Keywords:

NeuCode PTM identification intact mass lysine count modification proteoform quantification visualization

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Area of Science:

Proteomics
Systems Biology
Bioinformatics

Background:

Proteoforms, the distinct forms of proteins arising from genetic and post-translational modifications, play crucial roles in cellular functions.
Understanding proteoform dynamics is essential for deciphering complex biological processes and disease mechanisms.
Current analytical methods often face challenges in comprehensively identifying and quantifying diverse proteoforms within complex biological samples.

Purpose of the Study:

To introduce Proteoform Suite, an open-source, interactive software designed for the identification and quantification of proteoforms.
To enable the analysis of proteoform families, functional assessment via Gene Ontology (GO) analysis, and visualization of quantitative changes.
To demonstrate the utility of Proteoform Suite in uncovering systemic proteoform variations in response to environmental stress, using yeast salt stress as a model.

Main Methods:

Development of an open-source, interactive software program, Proteoform Suite.
Utilizing proteoform mass and intensity measurements from complex biological samples.
Employing Gene Ontology (GO) analysis for functional assessment of identified proteoform families.
Visualizing quantified proteoform families and their dynamic changes.

Main Results:

Proteoform Suite successfully identifies and quantifies proteoforms from complex biological data.
The software facilitates the construction of gene-derived proteoform families and their functional annotation.
Application to yeast salt stress reveals significant systemic proteoform variations, highlighting the tool's capability in stress response studies.

Conclusions:

Proteoform Suite provides a powerful, user-friendly platform for comprehensive proteoform analysis.
The tool aids in understanding the functional implications of proteoform diversity and dynamics.
This work demonstrates the potential of Proteoform Suite for investigating biological responses to various stimuli and conditions.