MSConvert filters for SWATH data

[sarkisi]

Hi! I am very new to coding and am attempting to convert my wiff2 SWATH data files to mzML format, with the goal to conduct unknown + retrospective data analysis. I wanted to know if there are best practice recommendations for applying filters prior to the conversion. As the acquisition is untargeted, I want minimal filters applied so that we can still capture everything. I am mainly looking to keep it at our acquisition windows (100-550 for precursor, 25-550 for SWATH), ionization mode, and a minimum peak height to filter out noise. I am not finding too much in the literature about how filters are applied specifically for SWATH data, so any help is truly appreciated.

[chambm]

It really depends what you're going to do with it in downstream analysis. You can always just convert without filters and see what you get with SeeMS or another viewer.