Johannes Rainer

The problem is that `featureSpectra` will not work because, AFAIK, you don't have a precursor m/z for the MS2 spectra in MSe. `featureSpectra` was developed for DDA and will return...

The `chromatogram` function is the suggested function to extract ion traces. It takes the parameters `rt`, `mz` and `msLevel` that allow you to specify the retention time window and the...

Actually, I just checked. The peak IDs of the MS2 chromatographic peaks used to build the reconstructed spectrum are in column `$ms2_peak_id` not `$peak_id` as detailed above. I will provide...

It turned out to be a little more complicated - I forgot that for SWATH we have MS2 spectra from different isolation windows, so there is an additional step required...

That's a good question. I would make sure to run several QC samples per measurement run, i.e. a pool of samples measured after every e.g. 8 injections. Just make sure...

If you have the same QCs in all your batches there is no problem in doing an alignment based on just these QC samples. There is the option to perform...

The fix was added to packages from Bioconductor release 3.8 and should be in there since. So, no need to specify `ref = "RELEASE_3_8"` in the `install_github` - actually, it's...

The problem you have with `PeakGroupsParam` is really strange. I guess this is independent of the subset-alignment and you get the same problem with the *conventional* full data set alignment?...

MS2 spectra get also adjusted along with the MS1 data (i.e. if you do the alignment in MS1, the retention time of the MS2 spectra gets also adjusted, based on...

@Adafede : you can *align* chromatographic data with the `alignRt` function - but that only allows small shifts between chromatograms. For DDA data, `xcms` performs the alignment on the MS1...