The effectiveness of filtering glycopeptide peak list files for Y ions

Chalkley, Robert J. and Medzihradszky F., Katalin and Darula, Zsuzsanna and Pap, Ádám and Baker, Peter R. (2020) The effectiveness of filtering glycopeptide peak list files for Y ions. MOLECULAR OMICS, 16 (2). pp. 147-155. ISSN 2515-4184

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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.

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