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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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The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

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Identification of modified peptides using localization-aware open search.

Fengchao Yu¹, Guo Ci Teo¹, Andy T Kong¹

¹Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.

Nature Communications

|August 15, 2020

Summary

This study introduces a localization-aware open search method for mass spectrometry, significantly improving the identification of modified peptides. The enhanced MSFragger tool offers greater sensitivity and accuracy in proteomics analysis.

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Last Updated: Dec 12, 2025

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Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Area of Science:

Proteomics
Mass Spectrometry
Biochemistry

Background:

Identifying modified peptides is vital but challenging in proteomics.
Current open search strategies struggle with modification localization and sensitivity.

Purpose of the Study:

To develop a localization-aware open search method for enhanced modified peptide identification.
To improve the sensitivity and accuracy of peptide modification analysis.

Main Methods:

Implemented a localization-aware open search strategy using MSFragger.
Integrated fragment ion indexing for both shifted and regular ions.
Developed a fast mass calibration and optimization method.

Main Results:

The enhanced MSFragger demonstrated significantly higher sensitivity and accuracy in identifying modified peptides.
The localization-aware approach improved modification site determination.
MSFragger outperformed other modification-focused tools in comprehensive searches.

Conclusions:

The localization-aware open search method with MSFragger is a powerful tool for sensitive and accurate modified peptide identification.
This advancement benefits shotgun proteomics by enabling more comprehensive analysis of post-translational modifications.