Roger Olivella Pujol

Dear ProteoWizard team, I'm converting RAW files from an Orbitrap Fusion Lumos to mzML and I realized that I'm losing a lot of sensitivity after aplying the PeakPicking filter. Our samples are a peptide mix of isotopologues (here for more info). For instance: 1) Peptide intensity with m/z = 428.2738 (RAW file viewed with Skyline): https://imgur.com/X8FPiHW 2) Same peptide intensity after msconvert (--32 --mzML --zlib): https://imgur.com/w404p8C 3) And same peptide again after msconvert with PeakPicking...