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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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Related Experiment Video

Updated: Aug 4, 2025

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

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics.

Daniel A Polasky¹, Daniel J Geiszler², Fengchao Yu¹

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

Molecular & Cellular Proteomics : MCP

|April 2, 2023

Summary

Identifying protein modifications is crucial for biology and disease research. A new MSFragger search engine mode improves the identification of various modified peptides, enhancing proteomic analysis.

Keywords:

fragmentation labile mass spectrometry phosphorylation post-translational modification proteomics search

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Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins

Published on: January 8, 2018

Area of Science:

Proteomics
Biochemistry
Molecular Biology

Background:

Posttranslational modifications (PTMs) are vital for protein function, regulating biological processes and disease states.
Mass spectrometry-based proteomics commonly uses database search methods for identifying modified peptides.
Traditional methods struggle with PTMs that fragment during tandem mass spectrometry, complicating spectral analysis.

Purpose of the Study:

To introduce a novel 'labile mode' in the MSFragger search engine.
To enhance the identification of modified peptides by tailoring searches to observed fragmentation patterns.
To improve the analysis of diverse posttranslational modifications.

Main Methods:

Development of a new 'labile mode' within the MSFragger search engine.
Tailoring modification-centric searches to specific fragmentation characteristics of PTMs.
Application of the labile mode to analyze phosphopeptides, RNA-crosslinked peptides, and ADP-ribosylated peptides.

Main Results:

The labile mode significantly improves spectrum identification rates for modified peptides.
Demonstrated enhanced identification for phosphopeptides, RNA-crosslinked peptides, and ADP-ribosylated peptides.
Showcased the adaptability of MSFragger's labile mode across various PTM types with distinct fragmentation patterns.

Conclusions:

MSFragger's labile mode offers a flexible and powerful approach for identifying a wide range of protein modifications.
This advancement improves the accuracy and efficiency of proteomic analyses in biological and disease research.
The method effectively addresses challenges posed by PTM fragmentation during mass spectrometry.