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Related Concept Videos

Proteomics01:33

Proteomics

7.4K
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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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
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The need for open and FAIR data in top-down proteomics.

Frederik Lermyte1

  • 1Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany.

Proteomics
|December 13, 2023
PubMed
Summary

Top-down proteomics (TDP) analysis generates vast datasets. TopDownApp offers a new open platform for visualizing and analyzing this complex proteomic data, improving data sharing and reuse.

Keywords:
FAIR datamass spectrometryopen sciencetop-down proteomics

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Area of Science:

  • Biochemistry
  • Proteomics
  • Computational Biology

Background:

  • High-throughput tandem mass spectrometry has advanced top-down proteomics (TDP).
  • The increasing scale of TDP studies necessitates improved data sharing and reuse.
  • Current data management practices pose challenges for large-scale proteomic initiatives.

Purpose of the Study:

  • To introduce TopDownApp, an open-source platform for TDP data analysis and visualization.
  • To facilitate more convenient and robust sharing and reuse of TDP data.
  • To support reanalysis of published datasets and machine learning model training.

Main Methods:

  • Development of a customizable, open platform named TopDownApp.
  • Implementation of visualization and analysis tools specifically for TDP data.
  • Focus on data interoperability and accessibility standards.

Main Results:

  • TopDownApp provides a centralized environment for TDP data exploration.
  • The platform aims to enhance the findability, accessibility, interoperability, and reusability (FAIR) of proteomic data.
  • Potential for reanalysis of existing datasets and training of machine learning algorithms.

Conclusions:

  • TopDownApp represents a significant step towards improved TDP data management.
  • Enhanced data sharing and interoperability are crucial for advancing proteomic research.
  • This platform could serve as a valuable resource for the TDP community.