Re: Centroiding of profile-mode DDA data, MS2-level
Reply #5 –
Thanks for the feedback - indeed we might have to check the code again. I've never centroided MS2 data so far.
The good news is that we've added the msLevel parameter to the pickPeaks method. This means you could call pickPeaks on your object with msLevel. = 1L to perform the centroiding only on MS 1 and keep the MS2 spectra as they are.
To use the new functionality you would however have to switch to the current Bioconductor developmental version:
BiocManager::install(version = "3.10")