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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 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,...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Updated: Jun 6, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

PRIDE and "Database on Demand" as valuable tools for computational proteomics.

Juan Antonio Vizcaíno1, Florian Reisinger, Richard Côté

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.

Methods in Molecular Biology (Clifton, N.J.)
|November 11, 2010
PubMed
Summary
This summary is machine-generated.

The Proteomics Identifications Database (PRIDE) offers rich proteomics data and metadata for exploring protein expression. New tools like Database on Demand and federated BioMart queries enhance data mining and integration capabilities.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • The Proteomics Identifications Database (PRIDE) is a key resource for mass spectrometry-based proteomics data.
  • It provides access to protein identifications, peptides, and modifications across diverse biological contexts.
  • Rich metadata is crucial for interpreting experimental data.

Purpose of the Study:

  • To describe the utility of the Database on Demand (DoD) tool for optimizing proteomics search engine results.
  • To demonstrate the potential of PRIDE for data mining through federated BioMart queries.
  • To showcase the integration of PRIDE data with other biological databases.

Main Methods:

  • Utilized the Database on Demand (DoD) tool for custom sequence database construction.
  • Performed federated BioMart queries to integrate PRIDE data with external resources like Ensembl, Reactome, and UniProt.
  • Explored complex querying strategies for enhanced data analysis.

Main Results:

  • Demonstrated successful optimization of search engine results using DoD.
  • Successfully integrated PRIDE data with multiple external biological databases.
  • Showcased the feasibility of complex data mining on proteomics datasets.

Conclusions:

  • PRIDE is a valuable resource for proteomics data exploration and analysis.
  • DoD enhances the utility of PRIDE by enabling custom database generation.
  • Federated BioMart queries facilitate comprehensive data mining and integration with other biological resources.