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"Ghost" fragment ions in structure and site-specific glycoproteomics analysis
Diana Campos1, Michael Girgis2, Qiang Yang3
1Max-Planck-Institut fuer Herz- und Lungenforschung, Ludwigstrasse 43, Bad Nauheim, 61231, Germany.
Biorxiv : the Preprint Server for Biology
|June 9, 2023
Summary
Glycopeptide analysis using mass spectrometry (MS) is challenging due to isobaric structures. This study identifies "Ghost" fragments that cause false positives, proposing a threshold to improve glycoproteomics accuracy.
Area of Science:
- Glycoproteomics
- Mass Spectrometry
- Structural Biology
Background:
- Glycosylation analysis via mass spectrometry (MS) is vital for understanding glycoproteins.
- Distinguishing isobaric glycopeptide structures remains a major challenge in glycoproteomics.
- Collision energy (CE) modulation has shown promise for qualitative glycopeptide analysis.
Approach:
- Investigated glycopeptide fragmentation specificity using synthetic stable isotope-labeled standards.
- Utilized isotopic labeling at the reducing terminal GlcNAc to differentiate fragment origins.
- Examined oxonium ion specificity and potential for false positive assignments.
Key Points:
- Identified "Ghost" fragments arising from glyco unit rearrangement or core fragmentation.
- Demonstrated that these fragments can lead to misidentification of glycan structures.
- Established a minimal intensity threshold to mitigate false positive structure assignments.
Conclusions:
- Developed a method to improve the accuracy of glycopeptide structure elucidation in MS.
- Mitigation of "Ghost" fragments is crucial for reliable glycoproteomics measurements.
- Findings advance the field towards more precise quantitative and qualitative glycoproteomics analysis.
