School of Biosciences, University of Sheffield, Sheffield, United Kingdom
Robert D Turner
Department of Computer Science, University of Sheffield, Sheffield, United Kingdom
Aline Rifflet
Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France; INSERM, Équipe Avenir, Paris, France; CNRS, UMR 2001 "Microbiologie intégrative et moléculaire", Paris, France
Adelina E Acosta-Martin
biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom
Andrew Nichols
Protein Metrics Inc, Cupertino, United States
Milena M Awad
Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Australia
Dena Lyras
Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Australia; Department of Microbiology, Monash University, Clayton, Australia
Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France; INSERM, Équipe Avenir, Paris, France; CNRS, UMR 2001 "Microbiologie intégrative et moléculaire", Paris, France
School of Biosciences, University of Sheffield, Sheffield, United Kingdom; biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom
Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan (PG), the essential and major component of bacterial cell envelopes. It icomprises glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGFinder for the analysis of PG structure and demonstrate that it represents a powerful tool to quantify PG fragments and discover novel structural features. Our analysis workflow, which relies on open-access tools, is a breakthrough towards a consistent and reproducible analysis of bacterial PGs. It represents a significant advance towards peptidoglycomics as a full-fledged discipline.
