Analysis of peptidoglycan structural diversity using LC-MS/MS and peptidoglycomics software

Peptidoglycan (PG) is a complex and essential macromolecule found in the bacterial
cell envelope. The structural analysis of PG requires the purification of this molecule
and its enzymatic digestion to produce disaccharide-peptides. PG fragments (called
muropeptides) are analysed by liquid chromatography coupled to mass spectrometry
(LC-MS/MS) and the structure of the intact molecule is inferred from the composition
of muropeptides and their crosslinking patterns. Despite tremendous progress in the
LC-MS/MS instrumentation, existing ‘Omics software are not suitable, and PG analysis
therefore, remains a mostly manual, tedious, biased, and error-prone process. This
work builds on the recent development of PGFinder, an open-access software tool
dedicated to PG analysis. Using bacteria displaying distinct PG compositions as model
systems, this work contributed to optimise LC-MS/MS conditions, the capabilities of
PGFinder and provided a detailed and consistent strategy for PG structural analysis.
This represents a major step towards making peptidoglycomics a full-fledged
discipline