My project

My project is focusing on the development of a novel analysis pipeline to study the structure of bacterial peptidoglycans by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS).

Peptidoglycan (PG) is a complex polymer made of glycan strands cross-linked by short peptide stems and is the target of the most relevant antibiotics ever discovered (beta-lactams and glycopeptides). The strategy for PG structure analysis described 30 years ago is time- and labor-consuming, precluding high-throughput comparative analyses. It involves enzymatic digestion of glycan strands, separation of disaccharide-peptides (muropeptides) by rp-HPLC followed by collection and analysis of individual peaks by mass spectrometry (MS). Detection and quantification of muropeptides by UV absorbance under-estimates the complexity of PG due to the large number of co-eluting PG fragments. In addition, the manual inspection of individual spectra has a limited capability to search for new PG components, likely biasing the analysis towards previously identified species.

We propose to combine the ultra-high resolution LC-MS/MS to an unbiased and automated analysis of fragmentation spectra to determine the structure of bacterial peptidoglycan. This work is carried out in collaboration with an industrial partner, Protein Metrics, a US-based company developing MS software solutions. The PhD project involves both lab work and computing sciences to customize several aspects of the existing MS analysis software for PG analyses.

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