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A software tool and strategy for peptidoglycomics, the high-resolution analysis of bacterial peptidoglycans via LC-MS/MS
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A software tool and strategy for peptidoglycomics, the high-resolution analysis of bacterial peptidoglycans via LC-MS/MS
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Journal Article
A software tool and strategy for peptidoglycomics, the high-resolution analysis of bacterial peptidoglycans via LC-MS/MS
2025
Overview
Peptidoglycan is an essential component of the bacterial cell envelope—a mesh-like macromolecule that protects the bacterium from osmotic stress and its internal turgor pressure. The composition and architecture of peptidoglycan is heterogeneous and changes as bacteria grow, divide, and respond to their environment. Though peptidoglycan has long been studied via LC-MS/MS, the analysis of this data remains challenging as peptidoglycan’s unusual composition and branching can’t be handled by proteomics software. Here we describe user-friendly open-source tools and a web interface for building peptidoglycan databases, performing MS searches, and predicting the MS/MS fragmentation of muropeptides. We then use
Rhizobium leguminosarum
to describe a step-by-step strategy for the high-resolution analysis of peptidoglycan. The unprecedented detail of
R. leguminosarum
’s peptidoglycan composition (>250 muropeptides) reveals even the subtlest remodelling between growth conditions. These new and easier to use tools enable more systematic analyses of peptidoglycan dynamics.
Peptidoglycan (PG) is an essential component of the bacterial cell envelope, however, the structural characterization of PG via mass spectrometry remains challenging. Here, the authors develop PGFinder, an open-source web application for the LC-MS/MS analysis of peptidoglycan, and describe a step-by-step analysis strategy using
Rhizobium leguminosarum
as a model.
