Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

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,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

MLMarker: a machine learning framework for tissue inference and biomarker discovery.

Genome biology·2026
Same author

iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.

Analytical chemistry·2026
Same author

Harnessing genomic and bioinformatics for surveillance of pathogens in Africa: a scoping review of existing training and gaps in training.

BMC infectious diseases·2026
Same author

Project ODIN: advancing environmental genomic surveillance for public health across sub-Saharan Africa.

The Lancet. Microbe·2026
Same author

omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation in bulk- and single-cell proteomics.

Nature communications·2026
Same author

The Peptonizer2000: Bringing Confidence to Metaproteomics.

Journal of proteome research·2026
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jun 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

Using the PRIDE proteomics identifications database for knowledge discovery and data analysis.

Philip Jones1, Lennart Martens

  • 1EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. pjones@ebi.ac.uk

Methods in Molecular Biology (Clifton, N.J.)
|December 17, 2009
PubMed
Summary
This summary is machine-generated.

The PRIDE database offers a platform for exploring mass spectrometry proteomics data across diverse species and conditions. New tools and algorithms enhance data submission and quality assessment for protein identification.

More Related Videos

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

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
07:44

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Related Experiment Videos

Last Updated: Jun 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

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

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
07:44

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Proteomics

Background:

  • The PRIDE database archives mass spectrometry-based proteomics experimental data.
  • Proteomics experiments provide insights into protein expression across various biological contexts.
  • Data submissions include protein, peptide, and modification identifications, often with supporting mass spectra.

Purpose of the Study:

  • To describe the PRIDE database as a research tool for exploring and comparing proteomics experiments.
  • To introduce enhancements in data submission tools and formats.
  • To present a novel algorithm for evaluating peptide identification quality.

Main Methods:

  • Utilizing the PRIDE database for data exploration and comparative analysis.
  • Employing the PRIDE Converter tool for data submission.
  • Applying a new algorithm for fragment ion annotation and spectral visualization.
  • Constructing complex queries via PRIDE BioMart for data integration.

Main Results:

  • PRIDE facilitates the exploration of protein expression data from diverse taxonomic groups, tissues, and disease states.
  • The PRIDE XML format has been updated to include fragment ion information.
  • A novel algorithm aids in annotating fragment ions and assessing peptide identification quality from tandem mass spectrometry.
  • PRIDE BioMart enables complex data queries and integration with external annotation resources.

Conclusions:

  • The PRIDE database serves as a valuable resource for proteomics research, enabling data comparison and analysis.
  • Enhanced tools and algorithms improve the quality and accessibility of proteomics data.
  • PRIDE supports the integration of diverse biological data, advancing proteomic research capabilities.