Oral Presentation AUS-oMicS 2025

GlyComboCLI: A Command Line Interface for High-Throughput Glycan Identification in Mass Spectrometry Data with Integration into Major Analysis Platforms (#116)

Maia I Kelly 1 2 , Ignatius Pang 3 , William P Klare 3 , Nicolle H Packer 4 5 6 , Kiyoko F Aoki-Kinoshita 7 8 , Christopher Ashwood 1
  1. Protea Glycosciences, Wollongong, Australia
  2. College of Computing, Georgia Institute of Technology, Atlanta, GA, USA
  3. Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
  4. School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
  5. ARC Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Macquarie University, Sydney, NSW, Australia
  6. ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
  7. Glycan and Life Systems Integration Center (GaLSIC), Soka University, Tokyo, Japan
  8. Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan

Rapid identification of glycans present in mass spectrometry (MS) samples is a cornerstone of glycomics research and is integral to robust glycomics analysis pipelines. The command line interface (CLI) of GlyCombo offers distinct advantages over a graphical interface for data analysis, particularly in the context of identifying and characterizing complex glycan structures from large-scale mass spectrometry experiments. While traditional web-based tools like GlycoMod utilize point-and-click interactions, GlyComboCLI enables researchers to rapidly process large-scale, complex MS datasets with greater efficiency and reproducibility.

Through text-based commands, glycomics researchers can automate the assignment of monosaccharide combinations, handle multiple adduct searches, and anticipate off-by-one errors - while simultaneously maintaining detailed records of their analytical workflows. This streamlined approach has been integrated into Galaxy, an accessible remote server that allows raw files to be converted and processed with a single click, making high-throughput glycan analysis more accessible to the broader research community. Furthermore, GlyComboCLI’s searching capabilities are being incorporated into GlyCosmos, a comprehensive web portal that integrates glycosciences with life sciences through its extensive standards, repositories, and data resources covering genes, proteins, lipids, pathways, and diseases. Previous integrations with Skyline have been carried through to the command line interface and exemplify the ability for GlyComboCLI to seamlessly integrate with modern glycomics research pipelines.

To demonstrate the utility of GlyComboCLI, we re-analysed a published GlycoPOST N-glycome dataset of 23 different mouse tissues, and reach similar conclusions as the original publication, identifying over 300 N-glycan compositions across 46 raw files in 20 hours runtime for an end-to-end data analysis pipeline comprised of msconvert, GlyComboCLI, and Skyline. This successful replication and rapid analysis time demonstrates GlyComboCLI’s potential to accelerate glycomics research while maintaining analytical rigor, paving the way for more comprehensive studies of glycan distributions across tissues and organisms.