Glycan Side Reaction May Compromise ETD-Based Glycopeptide Identification

Darula, Zsuzsanna and Medzihradszky F., Katalin (2014) Glycan Side Reaction May Compromise ETD-Based Glycopeptide Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 25 (6). pp. 977-987. ISSN 1044-0305

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Abstract

Tris(hydroxymethyl)aminomethane (Tris) is one of the most frequently used buffer ingredients. Among other things, it is recommended and is usually used for lectin-based affinity enrichment of glycopeptides. Here we report that sialic acid, a common 'capping' unit in both N- and O-linked glycans may react with this chemical, and this side reaction may compromise glycopeptide identification when ETD spectra are the only MS/MS data used in the database search. We show that the modification may alter N- as well as O-linked glycans, the Tris-derivative is still prone to fragmentation both in 'beam-type' CID (HCD) and ETD experiments, at the same time-since the acidic carboxyl group was 'neutralized'aEuro"it will display a different retention time than its unmodified counterpart. We also suggest solutions that-when incorporated into existing search engines-may significantly improve the reliability of glycopeptide assignments.

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