GlyCombo Enables Rapid, Complete Glycan Composition Identification across Diverse Glycomic Sample Types

Glycans are sugar-based
polymers found to modify biomolecules,
including lipids and proteins, as well as occur unconjugated as free
polysaccharides. Due to their ubiquitous cellular presentation, glycans
mediate crucial biological processes and are frequently sought after
as biomarkers for a wide range of diseases. Identification of glycans
present in samples acquired with mass spectrometry (MS) is a cornerstone
of glycomics research; thus, the ability to rapidly identify glycans
in each acquisition is integral to glycomics analysis pipelines. Here
we introduce GlyCombo (https://github.com/Protea-Glycosciences/GlyCombo), an open-source, freely available software tool designed to rapidly
assign monosaccharide combinations to glycan precursor masses including
those subjected to MS2 in LC-MS/MS experiments. GlyCombo was evaluated
across six diverse data sets, demonstrating MS vendor, derivatization,
and glycan-type neutrality. Compositional assignments using GlyCombo
are shown to be faster than the current predominant approach, GlycoMod,
a closed-source web application. Two unique features of GlyCombo,
multiple adduct search and off-by-one error anticipation, reduced
unassigned MS2 scans in a benchmark data set by 40%. Finally, the
comprehensiveness of glycan feature identification is exhibited in
Skyline, a software that requires predefined transitions that are
derived from GlyCombo output files.