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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Related Experiment Video

Updated: Jul 27, 2025

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

MASH Native: a unified solution for native top-down proteomics data processing.

Eli J Larson¹, Melissa R Pergande², Michelle E Moss²

¹Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, United States.

Bioinformatics (Oxford, England)

|June 9, 2023

Summary

This summary is machine-generated.

A new software, MASH Native, offers a unified solution for native top-down proteomics (nTDP) data analysis. This user-friendly tool integrates native mass spectrometry and top-down proteomics for comprehensive characterization of protein complexes and proteoforms.

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Last Updated: Jul 27, 2025

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

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

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Published on: April 1, 2017

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Published on: February 7, 2022

Area of Science:

Proteomics
Mass Spectrometry
Biochemistry

Background:

Native top-down proteomics (nTDP) combines native mass spectrometry (nMS) and top-down proteomics (TDP) for analyzing protein complexes and proteoforms.
Existing software solutions for nTDP data analysis are fragmented, hindering comprehensive characterization.
There is a need for a unified, user-friendly software package to streamline nTDP data processing.

Purpose of the Study:

To develop a unified and user-friendly software package for the analysis of native top-down proteomics data.
To provide a comprehensive solution for processing complex nTDP datasets, including database searching capabilities.

Main Methods:

Development of the MASH Native software package.
Integration of various data formats and analysis options within a single interface.
Implementation of deconvolution, database searching, and spectral summing functionalities.

Main Results:

MASH Native provides a unified solution for nTDP data analysis.
The software offers a user-friendly interface with database searching capabilities.
MASH Native supports diverse data formats and includes multiple analysis options for comprehensive characterization of protein complexes and proteoforms.

Conclusions:

MASH Native serves as a "one-stop shop" for characterizing native protein complexes and proteoforms.
The software addresses the lack of a unified and user-friendly platform for nTDP data analysis.
MASH Native is freely available with comprehensive documentation and tutorials.