Automatic determination of O-glycan structure from fragmentation spectra

Glycosylation is one of the most important classes of post-translational protein modifications, but the identification of glycans is difficult because of their branched structures and numerous isomers. We describe an algorithm called Cartoonist Two that proposes structures for O-linked glycans by automatically analyzing fragmentation mass spectra. Cartoonist Two improves upon previous glycan identification software primarily in its scoring function, which can more successfully distinguish among a number of similar structures. Cartoonist Two was designed and tested with FTICR mass spectra, and includes automatic recalibration and peak selection especially tuned for such data, yet it can be easily adapted to fragmentation spectra (MS² or MSⁿ) from other instrument types. On a validated test set of 34 SORI-CID MSⁿ FTICR spectra from Xenopus egg jelly, Cartoonist Two gave the manually determined structural assignment either the first or second highest score over 90% of the time. And for over 50% of these spectra, Cartoonist Two selected a unique highest scoring structure that agreed with the manually determined one.