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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...

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Updated: Sep 8, 2025

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

PepMapViz: a versatile toolkit for peptide mapping, visualization, and comparative exploration.

Zhenru Zhou¹, Qui T Phung¹, Corey E Bakalarski^1,2

¹Department of Proteomic and Genomic Technologies, Genentech, Inc., South San Francisco, CA 94080, United States.

Bioinformatics (Oxford, England)

|July 15, 2025

Summary

This summary is machine-generated.

PepMapViz is a new R package for visualizing peptide mapping data from mass spectrometry. It aids in understanding protein domains, modifications, and predicting immunogenicity for antibody therapies.

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Area of Science:

Proteomics and Bioinformatics
Immunology and Drug Development

Background:

Mass spectrometry is crucial for identifying peptides and analyzing protein modifications.
Visualizing peptide data across different analysis tools and experimental conditions is challenging.

Purpose of the Study:

To introduce PepMapViz, a versatile R package for peptide mapping and visualization.
To facilitate the import and analysis of peptide data from various mass spectrometry tools.
To enhance the prediction of immunogenicity for antibody-based therapies through visualization.

Main Methods:

PepMapViz imports peptide data from multiple mass spectrometry analysis tools.
The package maps peptides to parent protein sequences, highlighting domains and modifications.
Comparative visualization across experimental conditions is supported.

Main Results:

PepMapViz enables visualization of MHC-presented peptide clusters in antibody regions.
It aids in visualizing cross-software mass spectrometry results at the peptide level.
The package visualizes domain details and post-translational modification coverage.

Conclusions:

PepMapViz offers flexible peptide mapping and visualization capabilities.
It supports the analysis of complex proteomics data and aids in drug development.
The R package is freely available for use and further development.