I have been using the AccurateMassSearch node in my pipeline for a long time with no issues, but yesterday I noticed that the resulting annotations fall outside of the ppm error value defined in the dialogue.
More specifically, in negative ion mode the ppm threshold actually used is 3x higher than the inputted one, while in positive it is 2x higher.
I also tried to change the mass error value using a flow variable, but the result did not change.
I am working on win10, KNIME 4.3.1, OpenMS nodes v184.108.40.206009301213, OpenMS v2.6.0
Any idea why this is happening?
do you know if this is due to upgrading the version or could this problem already have existed in the previous version (and you just did not see this problem)?
In any case, I think for this kind of “algorithmic” problems we should move the discussion to the developer’s GitHub if you are ok with that. More people can jump in then.
Btw, I found this in the code:
// absolute mass error: the adduct itself is irrelevant here since its a constant for both the theoretical and observed mass
// ppm tolerance: the diff_mz accounts for it already (heavy adducts lead to larger m/z tolerance)
Are you using “ppm”? Can you check if this only happens with molecules that have heavier adducts?
I checked my old data from a PC with OpenMS 2.1 and it looks fine, the issue must have been introduced with one of the releases between 2.1 and 2.6. I will check with other people that use the same workflow to see which version they have installed, and hopefully be able to track it down!
Regarding your second question, yes I am using ppm but it happens with all adducts, so it does not seem to be related to some kind of correction for mz difference.
I followed your advice and opened an issue on github, you can find it here.