I am fairly inexperienced in Proteomics and am trying to transition my data analysis workflow into R. I'm following the tutorials according to the R for Mass Spectrometry initiative. Data in my lab are acquired such that files are .wiff and .wiff.scan (Sciex). To use packages such as Spectra I first convert these into .mzML with MSConvert (with peakPicking filter applied, if that is relevant). After I load this into R using the Spectra package I notice a lot of data are missing (namely the Precursor Scan Number of MS2 spectra). Keep in mind that this happens when I convert both DDA data and SWATH acquisition data (don't really know if the acquisition method has anything to do with this).

Is this information being lost in conversion or is it not recorded at all in Sciex files?

It is to be expected to have NA values in the MS1 scan's precursor metadata. These are only relevant for MS2 scans.

I'm not sure what you would see for SWATH data, but the same principles apply.