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The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
Published on: November 2, 2021
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Quantitative proteome-wide O-glycoproteomics analysis with FragPipe.
Daniel A Polasky1, Lei Lu2,3, Fengchao Yu4
1Department of Pathology, University of Michigan, Ann Arbor, MI, USA. dpolasky@umich.edu.
Analytical and Bioanalytical Chemistry
|June 14, 2024
Summary
This study introduces an improved O-glycoproteomics pipeline using the O-Pair method for sensitive and site-specific identification of O-glycopeptides. The new method enhances speed, accuracy, and quantification in glycopeptide analysis.
Area of Science:
- Biochemistry
- Proteomics
- Mass Spectrometry
Background:
- O-glycopeptide identification is challenging due to glycan dissociation during mass spectrometry.
- Existing methods struggle with site localization and quantification of O-glycopeptides.
Purpose of the Study:
- To develop an improved O-glycoproteomics pipeline for proteome-wide, site-specific, and quantitative analysis.
- To integrate the O-Pair method into the FragPipe platform for enhanced O-glycopeptide discovery.
Main Methods:
- Incorporation of the O-Pair method into the FragPipe pipeline.
- Utilizing both collisional and electron-based activation scans for peptide and glycan analysis.
- Implementation of oxonium ion-based filtering and support for diverse MS acquisition methods.
Main Results:
- Achieved enhanced speed and sensitivity in O-glycopeptide identification.
- Enabled site-specific localization and quantitative analysis of O-glycopeptides.
- Provided a comprehensive comparison of O-glycosite localization software.
Conclusions:
- The improved pipeline offers a robust solution for comprehensive O-glycoproteomics analysis.
- This advancement facilitates deeper insights into the functional roles of O-glycosylation.
