Johannes Rainer

That is actually a problem with `mzR` and more recent versions of proteowizard. Maybe try with the suggestions from this issue https://github.com/lgatto/MSnbase/issues/551 . In the longer run we hope to...

Seems that the converted file only contains a single chromatogram entry - which is the TIC (with the "non-standard data array" in it) - I guess the original file contains...

The developmental `mzR` version with an updated proteowizard code is [available](https://github.com/sneumann/mzR/tree/feature/updatePwiz_3_0_21263). With this version it should be possible to read the mzML files. It might take some time until this...

There is no alignment method as we have for `XCMSnExp` (i.e. spectra data) available for the chromatographic data. What is available is the `findChromPeaks` method that allows to identify chromatographic...

Could you please add here also the R code you used to perform this analysis. Without that it's impossible to replicate and find out what your problems might be.

Since the peaks are quite different (the first one broader the second quite narrow) I would suggest to use centWave instead of matchedFilter: ```r cwp

At present we don't have a dedicated function to do a retention time alignment on MRM data (similar to what is available for spectra-based LC-MS data). For chromatograms with a...

I would suggest to adapt the https://github.com/DorresteinLaboratory/XCMS3_FeatureBasedMN/blob/master/XCMS3_Preprocessing.Rmd file for your analyses. That is the most recent and complete file. The other two example Rmds seem to be outdated.

@tiwa1125 , could you please paste here the output of your `sessionInfo()` and ideally also the command you used to extract the spectra as well as the error message? Could...

Dear Tingting, great that you did this on publicly available data! This gives me the chance to replicate locally to exactly understand what is going on (wrongly). Unfortunately, the screenshots...