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Optimizing Waters HDMS Preprocessing for Metabolomics Pipelines

The user is facing difficulties in preprocessing Waters SYNAPT-G2 HDMS data for untargeted metabolomics analysis, specifically in converting raw data to .mzML format for downstream processing in XCMS. The main issue lies in choosing the correct conversion strategy using msconvert, balancing between centroiding and combining ion mobility spectra.

Science, Chemistry, Analytical Chemistry