Oliver Alka

Unfortunately, there are no merged spectra passed to SIRIUS. All spectra for a specific feature are passed via the SiriusMSFile, which is the SIRIUS internal format. SIRIUS merges them internally....

The concatenated nativeIDs are set as `NativeID` in the SiriusFragmentAnnotation. https://github.com/OpenMS/OpenMS/blob/develop/src/openms/source/FORMAT/DATAACCESS/SiriusFragmentAnnotation.cpp#L108 Yes, they correspond to the original nativeID in the mzML file (at least they should). Yes, ConsensusXML is not...

Hi @jpfeuffer, if you are using AccurateMassSearch, it is possible to have multiple initial molecular formula/adduct inputs based on MS1 identification for the same group of MS2 spectra. All of...

Yes, that is true, but it also resolves ambiguities introduced by multiple identifications for the same feature. Let's say you have one feature which has two possible AMS identifications (`ID1[C19H26O6,[M+Na]+]`;...

> Ah I see. But in that case there would never be multiple candidates reported by Sirius right? In that mode it only evaluates the one formula given to it...

@timosachsenberg unfortunately not yet - I will look into it.

@timosachsenberg I will probably not work on this anymore - can that be changed into an Hacktoberfest issue?

@Leon-Bichmann Would you be able to add a minimal example (with an example file and bash script). I rebuild Lukas version and would like to test if the issue persists.

Ok, so it seems to be an issue of our standalone version of SpectraST. Unfortunately, I was not yet able to localize the culprit. I tested TPP 5.0 and TPP...

I have tried, but was not yet able to compile a working standalone SpectraST version using a newer TPP version @lukaszimmermann has done that before, but I am not sure...