Julianus Pfeuffer

I think you have to add the mods as CUSTOM0..CUSTOM9 to the unimod.xml in the OpenMS share.

I think this is a comet specific extension, right? It sounds like this is a MS1 offset only. I am not sure if it will consider those offsets for every...

> > I think you have to add the mods as CUSTOM0..CUSTOM9 to the unimod.xml in the OpenMS share. > > But can this be done dynamically, or we need...

> by default search engines assume that the mass shift on the precursor is also observed on the fragments carrying the PTM (e.g., no neutral loss on the PTM is...

Yes it's supported. You will need to add the custom unimod.xml to every step though. You can just add the XML entry with echo "\" \>\> Openmsshare/unimod.xml No, it is...

Hmm yes, I think we should support this. We could either allow this in level 3 spectra generally (is it the level 3 spectra?) or we count the number of...

Quick question: Since isolation windows are not mandatoryin mzML, why not leave them out, when it cannot be extracted reliably? I assume -0.5 is just a placeholder for "failed" since...

Thanks for the clarification. @timosachsenberg @cbielow Should we then just remove the non-negativity check and hope that none of the algorithms/visualizations fail? Or we force it to 0? In THEORY,...

Aah! Yes exactly, that was my point. I think I would prefer not reporting the element in the case the extraction fails/does not make sense. Yes, `IsobaricAnalyzer` does use it...

Hi! You seem to have no proteins left in ProteomicsLFQ. You don't need to filter for proteins before you performed inference (done inside of ProteomicsLFQ). You might also need to...