Johannes Rainer

I made a pull request on `combineSpectra` on `MSnbase` - let's hope that gets into it soon (today?).

An update to illustrate what's possible with the `combineSpectra` from PR https://github.com/lgatto/MSnbase/pull/367 The idea is to first get all MS2 spectra for all chromatographic peaks associated to a feature from...

I am currently working on the `spectra_methods` branch of MSnbase. But there might still be some updates/changes we need to make. Ultimately you will no longer need this for loop,...

Thanks for the feedback @cbroeckl ! As mentioned by @michaelwitting , it would be nice if you could share one file for testing purposes (along with some explanations). we've implemented...

Thanks @cbroeckl , I'll have a look at it and come back to you if I have questions.

Nice suggestion @cbroeckl . What puzzles me is that `precursorIntensity` in your `Spectrum2` object is `0` - This should be extracted correctly from the mzML.

I guess the solution to this would be to update the proteowizard version within `mzR` - and if I'm not wrong @sneumann tried to do that already but stumbled across...

also, restricting on RT might have an influence on the background signal detection which is used for parameter `snthresh`.

Note that the `ppm` parameter in centWave has a slightly different meaning: it's used in the first step of the peak detection and it is the acceptable deviation of individual...

`msLevel = 0`? so the *mzXML* files still have spectra in it? What's the difference between MS1 and MS0? Can one assume such spectra are equivalent?