Filtering MS2 datasets on the basis of MS1 peak intensities

[gaiburg]

I am trying to polish my metabolomics MS2 files in order to produce data visualisation to facilitate data exploration. I have been using the mass detection feature, where I set a threshold on the mass detection option according to the level of noise I would like to get rid of in my MS1 spectrum. I then do the same for my MS2 data, setting the noise to 0.0 as I want to keep all the MS2 peaks generated by the filtered MS1 parent peaks. I however end up with an equal number of peaks as the original .mzML file uploaded onto the workspace. I would also like to obtain this filtered dataset as an .mzML, and I seem to only be able to do this from the two separate masslists obtained from mass detection (ms1 and ms2). Can anyone help?