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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...
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...
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,...
Rapid Identification of Pathogens01:25

Rapid Identification of Pathogens

MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...

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Related Experiment Video

Updated: Jun 18, 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 Proteomics Identifications database: 2010 update.

Juan Antonio Vizcaíno1, Richard Côté, Florian Reisinger

  • 1EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Nucleic Acids Research
|November 13, 2009
PubMed
Summary
This summary is machine-generated.

The Proteomics Identifications database (PRIDE) offers enhanced features for mass spectrometry proteomics data submission and visualization. It now supports fragment ion annotations and integrates with multiple biological resources for powerful cross-domain queries.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • The Proteomics Identifications database (PRIDE) is a major repository for mass spectrometry-derived proteomics data.
  • PRIDE has experienced substantial growth, holding extensive data on multiple species and millions of protein identifications, peptides, and spectra.

Purpose of the Study:

  • To describe new and improved features in the PRIDE database.
  • To highlight advancements in data submission, visualization, and integration capabilities.

Main Methods:

  • Implemented a revised submission process for proteomics data.
  • Enabled direct submission and visualization of fragment ion annotations on tandem mass spectra.
  • Developed the PRIDE BioMart interface for integrative queries with external biological resources.

Main Results:

  • PRIDE now facilitates direct submission and visualization of fragment ion annotations, aiding compliance with data submission requirements.
  • The PRIDE BioMart interface allows powerful cross-domain queries, integrating PRIDE data with resources like Reactome, Ensembl, InterPro, and UniProt.
  • The database has grown significantly, encompassing diverse species and millions of proteomic data points.

Conclusions:

  • Enhanced features in PRIDE improve data submission, analysis, and integration within the proteomics field.
  • The ability to perform integrative queries is crucial for future bioinformatics analyses.
  • PRIDE's integration with other databases underscores the importance of data sharing in proteomics research.