The metaproteomics workflow for microbiome characterization should be improved at the level of mass spectrometry to obtain as much information as possible. Starting point is the results our group published in 2024 for the characterization of fecal samples by Orbitrap-Astral technology with more than 120,000 peptides identified and quantified in a single DIA acquisition run (Dumas et al., 2024). Novel fractionation of samples, new data acquisition modes, additional filters such as FAIMS and PASEF ion mobility, and numerous parameters for acquiring mass spectrometry will be explored with standardized microbiome models and tuned to maximize the results with the latest generation of instruments. Methods will be benchmarked and their robustness will be documented.
Maximizing the acquisition of interpretable data is of utmost interest to gain further biological insights into each sample that metaproteomics could analyze. Here, the optimized workflow and methods will benefit all the other projects of the METAMIC3 consortium. To achieve this objective, the PhD candidate will be engaged in cross-disciplinary collaboration with other researchers, test samples representative of the different samples treated in the METAMIC3 consortium and participate in close relationships with software developers to evolve tools for higher coverage of metaproteomics.