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Updated: Jun 1, 2026
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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses
Mathieu Courcelles1, Sébastien Lemieux, Laure Voisin
1IRIC, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, Canada; Department of Biochemistry, Université de Montréal, Montréal, Canada.
Proteomics
|June 2, 2011
Summary
ProteoConnections is a new bioinformatics platform that organizes proteomics data, evaluates quality, and aids interpretation. This tool enhances the analysis of large-scale proteomics and phosphoproteomics datasets for biological discovery.
Area of Science:
- Bioinformatics
- Proteomics
- Computational Biology
Background:
- Large-scale proteomics data requires advanced computational tools for biological insights.
- Existing bioinformatics platforms often lack comprehensive features for proteomics analysis.
Purpose of the Study:
- To develop ProteoConnections, a bioinformatics platform for organizing, evaluating, and interpreting proteomics data.
- To facilitate the analysis of phosphoproteomics data, including site annotation and kinase motif identification.
Main Methods:
- Development of a relational database for storing peptide and protein identifications.
- Integration of post-translational modification (PTM) databases and bioinformatics tools.
- Application of ProteoConnections to phosphoproteomics data from rat intestinal IEC-6 cells.
- Quantitative proteomics data integration for analyzing phosphorylation changes.
Main Results:
- Identification of 9615 phosphorylation sites on 2108 phosphoproteins in rat intestinal cells.
- Annotation of phosphorylation sites based on kinase motifs, conservation, and protein context.
- Revealed biological insights into phosphoprotein regulation, including altered protein interactions.
Conclusions:
- ProteoConnections effectively organizes and analyzes complex proteomics and phosphoproteomics data.
- The platform accelerates data interpretation and provides valuable biological insights.
- Enables quantitative analysis of phosphorylation changes in response to stimuli or inhibitors.
Related Concept Videos
01:33Proteomics
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 proteomics...
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 proteomics...
02:26Protein Networks
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,...
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,...
02:26Protein Networks
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,...
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,...
02:04Protein-protein Interfaces
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 polypeptide...
02:04Protein-Protein Interfaces
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 polypeptide...
02:54Protein Kinases and Phosphatases
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...