Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry

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 Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Protein-protein Interfaces

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...

You might also read

Related Articles

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

Sort by

Same author

Knowledge Graph-Driven AI in Biohealth: From Biomedical Discovery to Health Risk Prediction.

Delaware journal of public health·2026

Same author

Enhanced Adverse-Event Detection and Drug-Event Relation Extraction from Clinical Notes.

medRxiv : the preprint server for health sciences·2026

Same author

A network-centric approach reveals novel pathways impacted by Prader-Willi Syndrome.

PloS one·2026

Same author

The Common Fund Data Ecosystem (CFDE).

bioRxiv : the preprint server for biology·2026

Same author

Pretraining effective T5 generative models for clinical and biomedical applications.

PloS one·2026

Same author

Desiderata for a biomedical knowledge network: opportunities, challenges and future directions.

Bioinformatics advances·2026

Search research articles

Related Experiment Video

Updated: May 8, 2026

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

A fast Peptide Match service for UniProt Knowledgebase.

Chuming Chen¹, Zhiwen Li, Hongzhan Huang

¹Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneva 4, Switzerland.

Bioinformatics (Oxford, England)

|August 21, 2013

Summary

A new web application, Peptide Match, enables rapid retrieval of query peptides from UniProt Knowledgebase (UniProtKB). This tool enhances proteomic data analysis by linking matched proteins to spectral databases and offering flexible search options.

More Related Videos

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Peptide-based Identification of Functional Motifs and their Binding Partners

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Related Experiment Videos

Last Updated: May 8, 2026

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Peptide-based Identification of Functional Motifs and their Binding Partners

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Area of Science:

Bioinformatics
Computational Biology
Proteomics

Background:

Existing methods for peptide matching can be time-consuming.
There is a need for efficient tools to query large protein databases.

Purpose of the Study:

To develop a fast and comprehensive web application for peptide matching.
To integrate UniProt Knowledgebase (UniProtKB) data with other proteomic resources.

Main Methods:

Developed a web application utilizing an Apache Lucene-based search engine.
Implemented features for handling isoforms, isobaric amino acids (leucine/isoleucine), and UniRef100 sequences.
Integrated dynamic queries to major proteomic databases.

Main Results:

The Peptide Match service quickly retrieves all occurrences of a query peptide from UniProtKB.
Matched proteins are presented in annotated summary tables with links to spectral databases.
Results are organized by taxonomy, enabling browsing by organism or taxonomic group.

Conclusions:

The Peptide Match service offers an efficient solution for peptide identification and analysis.
The application provides a user-friendly interface and RESTful web services.
Data is regularly updated to reflect the latest UniProt releases.