MS2 and higher spectra should be filtered according to precursor m/z and RT. The MzMLFile, MzDataFile, MzXMLFile have to be changed for that (Hiwi) Currently when specifying mz or RT filters, they will also be applied to MS levels >=2 (not really what you usually want). To work around this, you need to extract the MS2 levels beforehand, do the filtering on MS1 and merge them back together.