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Related Concept Videos

Proteomics01:33

Proteomics

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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.
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Related Experiment Video

Updated: Nov 4, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics

Robert W Seymour1, Sjoerd van der Post1,2, Arshag D Mooradian1

  • 1Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States.

Journal of Proteome Research
|May 31, 2021
PubMed
Summary
This summary is machine-generated.

ProteoSushi is a new software tool that analyzes peptide-centric proteomic data for post-translational modifications (PTMs). It simplifies data processing and enhances knowledge discovery from large-scale PTM proteomics datasets.

Keywords:
PTMsacetylationbioinformaticschemoproteomicsmodification-specific proteomicsphosphorylationpost-translational modificationsproteomicsproteosushi

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Area of Science:

  • Proteomics
  • Biochemistry
  • Bioinformatics

Background:

  • Post-translational modifications (PTMs) are crucial for cell signaling and disease.
  • Current proteomics software struggles with peptide-centric data from PTM enrichment workflows.

Purpose of the Study:

  • To develop ProteoSushi, a software tool for analyzing peptide-centric PTM proteomics data.
  • To overcome limitations in evaluating and interpreting PTM data.

Main Methods:

  • ProteoSushi assigns identified peptides to proteins/genes, minimizing redundancy.
  • It simplifies quantitation by aggregating intensities for each modified site.
  • The tool annotates PTM sites with biological information from UniProt.

Main Results:

  • ProteoSushi streamlines processing of large PTM proteomics datasets.
  • It facilitates knowledge mining by integrating diverse biological annotations.
  • The software offers a user-friendly graphical interface.

Conclusions:

  • ProteoSushi enhances the analysis of modification-specific proteomics data.
  • It provides a flexible and comprehensive solution for PTM site analysis.
  • The tool supports various PTMs and chemical labels.