Johannes Rainer

@stanstrup is right. The reason for your error essentially is that `MSnbase` does not know what to do with a MS level 0 data. The *old* `xcms` did not really...

In which file format do you have your data? one possiblity would be to replace the MS0 with MS1 in the raw data files... or maybe read them with `Spectra`,...

Data structures for identified chrom peaks: - it is possible to add arbitrary annotations to each chromatographic peak using the `chromPeakData` `DataFrame`. Default columns in that `DataFrame` are `ms_level` and...

Peak detection within isolation windows is possible with the `findChromPeaksIsolationWindow` function. The isolation window (i.e. definition which spectra belong to which isolation window) can be specified with the `isolationWindow` parameter.

For each MS1 peak we have then to - identify fragment candidates (MS2 peaks) within the same rt window. - extract chromatogram for all - align chromatograms - correlate chromatograms...

Yes @sneumann ! That would be awesome! So far I am @michaelwitting 's toy data set and I was trying to talk him into adding that to the `msdata` package.

Actually, it might still be helpfull to add one SWATH mzML file to `msdata` to have something for the unit tests...

@sneumann, can you share the `mtbls297` package somehow?

The code to *align* `Chromatogram` objects and to correlate them will be implemented in methods #379 and #380 - these might eventually then go to `MSnbase`.

agree - but I would do this in a second step. IMHO it would be easier (and safer) to define the MS2 spectrum for each chromatographic peak (in each file)...