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Related Concept Videos

Proteomics01:33

Proteomics

10.2K
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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Peptide Identification Using Tandem Mass Spectrometry01:33

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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Updated: Mar 29, 2026

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
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MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.

Wenxuan Cai1, Huseyin Guner2, Zachery R Gregorich1

  • 1From the ‡Department of Cell and Regenerative Biology, §Molecular Pharmacology Training Program.

Molecular & Cellular Proteomics : MCP
|November 25, 2015
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Summary

Top-down mass spectrometry (MS) enables comprehensive proteoform analysis but faces data interpretation challenges. MASH Suite Pro software simplifies this by integrating identification, quantitation, and characterization tools for high-resolution MS data.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Top-down mass spectrometry (MS) is crucial for analyzing proteoforms, including those from genetic variation, alternative splicing, and posttranslational modifications (PTMs).
  • High-resolution MS data complexity poses significant analytical challenges, with underdeveloped software tools compared to bottom-up proteomics.
  • A multifunctional platform for identification, quantitation, and characterization of proteoforms with visual validation is currently lacking.

Purpose of the Study:

  • To develop MASH Suite Pro, a comprehensive software tool for top-down proteomics.
  • To address the need for integrated data analysis, including identification, quantitation, and characterization of proteoforms.
  • To provide visual validation components for accurate interpretation of complex MS data.

Main Methods:

  • Developed MASH Suite Pro, a software tool for processing high-resolution MS and tandem MS (MS/MS) data.
  • Integrated two deconvolution algorithms to optimize protein identification.
  • Incorporated functionalities for PTM and sequence variation characterization, relative quantitation, and visual validation.

Main Results:

  • MASH Suite Pro processes high-resolution MS/MS data using dual deconvolution algorithms for enhanced protein identification.
  • The software facilitates characterization of PTMs, sequence variations, and relative quantitation of proteoforms across conditions.
  • Integrated visualization tools aid in the validation and correction of computational outputs, simplifying data reporting.

Conclusions:

  • MASH Suite Pro offers a user-friendly interface for identification, quantitation, characterization, and visual validation in top-down proteomics.
  • The software significantly simplifies and accelerates the interpretation of complex high-resolution top-down proteomics data.
  • MASH Suite Pro is poised to advance the field of top-down proteomics by providing a versatile analytical platform.