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

7.6K
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...
7.6K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

6.6K
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...
6.6K
Protein Networks02:26

Protein Networks

4.0K
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,...
4.0K

You might also read

Related Articles

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

Sort by
Same author

Crosstalk in the kidney-muscle axis: myokines and muscle-relevant mediators in chronic kidney disease-associated sarcopenia.

Frontiers in medicine·2026
Same author

3M-052 combined inhibitory anti-TNFR2 synergistically suppresses colon cancer progression.

Frontiers in immunology·2026
Same author

ClpC1-dependent iron homeostasis underlies mycobacterial defense against oxygen-driven Fenton reaction during reactivation.

Microbiology spectrum·2026
Same author

Influence of trough currents on Permian reef-shoal belts and reef-capping dolomite reservoirs, Damaoping Block, Sichuan Basin, China.

Scientific reports·2026
Same author

Temperature Dominates Light in Regulating Lycopene During a Critical Period in Postharvest Tomato Fruit.

International journal of molecular sciences·2026
Same author

Reconfigurable terahertz metasurface based on photoconductive silicon and vanadium dioxide for broadband absorption and multiband polarization conversion.

Applied optics·2026
Same journal

OmicsTransformer: Self-Supervised Masked Consistency and Uncertainty-Aware Fusion for Robust Multi-Omics Prediction.

Bioinformatics (Oxford, England)·2026
Same journal

Computational Tool Choice Impacts CRISPR Spacer-Proto spacer Detection.

Bioinformatics (Oxford, England)·2026
Same journal

ARISE: RNA-Anchored Shared-Edge Topology and Hierarchical Fusion for Spatial Multi-Omics Integration.

Bioinformatics (Oxford, England)·2026
Same journal

Interactive exploration of biobank-scale ancestral recombination graphs with Lorax.

Bioinformatics (Oxford, England)·2026
Same journal

PepMCP: A Graph-Based Membrane Contact Probability Predictor for Membrane-Lytic Antimicrobial Peptides.

Bioinformatics (Oxford, England)·2026
Same journal

ARGscape: A modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Aug 11, 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

12.8K

Patpat: a public proteomics dataset search framework.

Weiheng Liao1, Xuelian Zhang1

  • 1State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.

Bioinformatics (Oxford, England)
|February 6, 2023
PubMed
Summary
This summary is machine-generated.

Researchers can now find proteins more easily using Patpat, a new framework that searches multiple proteomics databases. This tool enhances data discoverability in mass spectrometry research.

More Related Videos

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

12.8K
A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

696

Related Experiment Videos

Last Updated: Aug 11, 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

12.8K
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

12.8K
A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

696

Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • The FAIR principles (Findable, Accessible, Interoperable, Reusable) are increasingly important in proteomics.
  • Public proteomics databases offer Application Programming Interfaces (APIs) for data access.
  • Existing methods can be challenging for researchers to navigate vast mass spectrometry datasets.

Purpose of the Study:

  • To introduce Patpat, an extensible framework for searching public proteomics datasets.
  • To improve the findability of proteomics data by merging results from multiple databases.
  • To provide researchers with a streamlined method for identifying proteins of interest.

Main Methods:

  • Developed an extensible framework named Patpat.
  • Implemented a 2D strategy for combining search results from multiple public proteomics databases.
  • Utilized protein identifiers as input for retrieving metadata from relevant datasets.

Main Results:

  • Patpat enables efficient searching and merging of data from various proteomics databases.
  • The framework successfully improves the 'Findable' aspect of proteomics data.
  • Researchers can obtain metadata for relevant datasets using only protein identifiers.

Conclusions:

  • Patpat offers a novel solution for navigating and searching large-scale proteomics data.
  • The framework enhances data discoverability and accessibility for the research community.
  • Patpat supports the broader adoption and application of FAIR principles in proteomics.