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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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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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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Updated: May 28, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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ProteoArk: A One-Pot Proteomics Data Analysis and Visualization Tool for Biologists.

Mahammad Nisar1, Sreelakshmi Pathappillil Soman2, Sourav Sreelan1

  • 1Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, Karnataka 575018, India.

Journal of Proteome Research
|February 10, 2025
PubMed
Summary
This summary is machine-generated.

ProteoArk is a user-friendly web tool for mass spectrometry proteomics data analysis. It offers comprehensive pipelines for differential expression, functional enrichment, and visualization, simplifying complex bioinformatics workflows for researchers.

Keywords:
bioinformatics toolsdata analysisdata visualizationmass spectrometryproteomicsweb application

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Mass spectrometry-based proteomics generates large datasets requiring specialized analysis tools.
  • Existing tools often lack integration, requiring users to combine multiple software packages.
  • Streamlining proteomics data analysis is crucial for efficient biological discovery.

Purpose of the Study:

  • To develop ProteoArk, a unified web-based platform for comprehensive proteomics data analysis and visualization.
  • To provide accessible computational pipelines for both label-free and labeled (SILAC/iTRAQ/TMT) mass spectrometry data.
  • To simplify complex analyses, including differential expression, functional enrichment, and figure generation for researchers with basic bioinformatics skills.

Main Methods:

  • ProteoArk integrates four primary analysis sections: data processing, differential expression, functional enrichment, and visualization.
  • The platform supports postprocessing of search results from Proteome Discoverer, MaxQuant, and MSFragger.
  • Functional enrichment includes gene ontology, protein-protein interactions, and pathway analysis with various statistical tests.

Main Results:

  • ProteoArk offers user-friendly interfaces for analyzing label-free and labeled proteomics data.
  • The tool facilitates manuscript-ready figure generation (PCA, heatmaps, volcano plots) with a single click.
  • It streamlines complex workflows, making advanced proteomics analysis accessible to users with basic bioinformatics skills.

Conclusions:

  • ProteoArk provides a robust, integrated, and accessible solution for mass spectrometry-based proteomics data analysis.
  • The platform simplifies data interpretation and visualization, accelerating biological insights.
  • Freely available online and via Docker, ProteoArk enhances the accessibility of advanced proteomics tools.