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Related Concept Videos

Proteomics01:33

Proteomics

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...
Protein-protein Interfaces02:04

Protein-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...
Protein-Protein Interfaces02:04

Protein-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...
Protein Networks02:26

Protein 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,...
Protein Networks02:26

Protein 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,...
The Proteasome Structure01:17

The Proteasome Structure

The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
The proteasome is an...

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Related Experiment Video

Updated: May 17, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events.

Niklaas Colaert1, Davy Maddelein, Francis Impens

  • 1Department of Medical Protein Research, VIB, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.

Nucleic Acids Research
|October 25, 2012
PubMed
Summary

The Online Protein Processing Resource (TOPPR) is a new database detailing thousands of protein cleavage sites identified using COmbinded FRActional DIagonal Chromatography proteomics. It offers data visualization, analysis tools, and multiple search functionalities for researchers.

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Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

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Related Experiment Videos

Last Updated: May 17, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
10:05

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

Area of Science:

  • Proteomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Proteolytic processing is crucial for protein function and regulation.
  • Identifying and cataloging these cleavage events is essential for understanding cellular mechanisms.
  • Existing resources may lack comprehensive data on proteolytically processed sites.

Purpose of the Study:

  • To introduce The Online Protein Processing Resource (TOPPR), a novel database.
  • To provide a centralized repository for published proteolytically processed sites in human and mouse proteins.
  • To offer advanced analysis tools for protease specificity and substrate-centric studies.

Main Methods:

  • Utilized COmbinded FRActional DIagonal Chromatography (COFRADIC) proteomics technologies to identify cleavage events.
  • Developed an online database with full data provenance, including interactive mass spectrum visualization.
  • Implemented multiple data retrieval methods: by stimulus/assay, UniProtKB accession, or motif search.

Main Results:

  • Compiled a database of thousands of published proteolytically processed sites.
  • Integrated interactive visualization of fragmentation mass spectra with annotations and scores.
  • Enabled substrate analysis with annotations like secondary structure, domains, and 3D structures.

Conclusions:

  • TOPPR serves as a valuable, publicly accessible resource for proteomic data.
  • The database facilitates research into protease specificity and protein processing.
  • It enhances the understanding of protein function and regulation through detailed cleavage site information.