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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...

Peptide Bonds

Peptide Bonds

A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...

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Related Experiment Video

Updated: Apr 16, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

PeptideVisualizer: A Novel Software Solution for PROTOMAP Analysis.

Matej Kolarič^1,2, Sara Ivanovski^1,2, Tilen Sever^1,2

¹Jožef Stefan International Postgraduate School, Jamova 39, SI-1000 Ljubljana, Slovenia.

Journal of Proteome Research

|April 15, 2026

Summary

This summary is machine-generated.

PeptideVisualizer is new open-source software for proteomic analysis. It visualizes mass spectrometry data, protein structure, and peptide abundance to identify proteolytic events.

Keywords:

MaxQuant PROTOMAP PeptideVisualizer mass spectrometry open-source software proteolysis

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Last Updated: Apr 16, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

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

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Proteomic analysis generates large datasets.
Visualizing peptide and protein data is crucial for understanding biological processes.
Existing tools may lack comprehensive integration of quantitative and structural information.

Purpose of the Study:

To introduce PeptideVisualizer, an open-source software for PROTOMAP analysis.
To provide an intuitive platform for visualizing mass spectrometry data, protein secondary structure, and UniProt features.
To enable the assessment of proteolytic events using sequence context and peptide abundance.

Main Methods:

Processing of mass spectrometry data output from MaxQuant.
Visualization of protein migration in polyacrylamide gel electrophoresis and sequence coverage.
Integration of protein secondary structure and UniProt database information into peptographs.
Development of a novel mismatch factor for identifying proteolytic events.

Main Results:

PeptideVisualizer successfully visualizes complex proteomic data.
The software integrates quantitative information and handles multiple experiments with biological replicates.
The novel mismatch factor effectively identifies proteolytic events.
Validation on an apoptosis-related dataset demonstrated the software's utility.

Conclusions:

PeptideVisualizer is an effective and useful tool for large-scale proteomic data analysis.
The software facilitates the assessment of proteolytic events through integrated data visualization.
Its open-source nature and comprehensive features support advancements in proteomics research.