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Related Experiment Video

Updated: May 17, 2026

A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues

A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues

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Automated phosphopeptide identification using multiple MS/MS fragmentation modes.

Mathias Vandenbogaert¹, Véronique Hourdel, Olivia Jardin-Mathé

¹Systems Biology Lab, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France.

Journal of Proteome Research

|October 26, 2012

Summary

This summary is machine-generated.

Identifying phosphopeptides remains challenging. This study introduces FragMixer, a computational tool that combines different fragmentation spectra (CID, ETD, HCD) to improve amino acid sequence and phosphosite identification accuracy.

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Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)

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Published on: December 20, 2010

Area of Science:

Proteomics
Mass Spectrometry
Bioinformatics

Background:

Phosphopeptide identification is difficult due to insufficient fragment ions in mass spectrometry.
Current automated tools for paired spectra interpretation lag behind experimental advancements.

Purpose of the Study:

To assess an approach combining paired CID spectra (with/without multistage activation) for phosphopeptide analysis.
To develop an automated computational tool for reconciling and improving phosphopeptide identifications.

Main Methods:

Acquisition of paired CID spectra (MSA/MS2) on a LTQ-Orbitrap instrument.
Application on phosphopeptide samples from Arabidopsis thaliana of varying complexity.
Development of the FragMixer software for reconciling database search results using filtering rules.

Main Results:

FragMixer effectively reconciles sequence and phosphosite identifications from paired spectra.
Combining fragmentation schemes on precursor ions improves identification efficiency and phosphosite localization accuracy.
The software successfully analyzed phosphopeptide samples of moderate complexity.

Conclusions:

The FragMixer approach enhances phosphopeptide identification and phosphosite localization.
FragMixer offers flexible configuration and can be applied to various spectrum pairs (e.g., MSA/ETD, ETD/HCD).
The software is openly accessible, promoting wider adoption in proteomics research.