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Issue 2, 2020

The effectiveness of filtering glycopeptide peak list files for Y ions

Author affiliations

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

Supplementary files

Article information


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

Mol. Omics, 2020,16, 147-155
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, 16, 147 DOI: 10.1039/C9MO00178F

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