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The effectiveness of filtering glycopeptide peak list files for Y ions

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Abstract

Intact glycopeptide analysis is becoming more common with developments in mass spectrometry instrumentation and fragmentation approaches. In particular, collision-based fragmentation approaches such as higher energy collisional dissociation (HCD) and radical-driven fragmentation approaches such as electron transfer dissociation (ETD) provide complementary information, but bioinformatic strategies to utilize this combined information are currently lacking. In this work we adapted a software tool, MS-Filter, to search HCD peak list files for predicted Y ions based on matched EThcD results to propose additional glycopeptide assignments. The strategy proved to be extremely powerful for O-glycopeptide data, and also of benefit for N-linked data, where it allowed rescue of low confidence results from database searching.

Graphical abstract: The effectiveness of filtering glycopeptide peak list files for Y ions

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Article information


Submitted
09 Dec 2019
Accepted
06 Feb 2020
First published
06 Feb 2020

Mol. Omics, 2020, Advance Article
Article type
Research Article

The effectiveness of filtering glycopeptide peak list files for Y ions

R. J. Chalkley, K. F. Medzihradszky, Z. Darula, A. Pap and P. R. Baker, Mol. Omics, 2020, Advance Article , DOI: 10.1039/C9MO00178F

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