Julianus Pfeuffer
Julianus Pfeuffer
True! Zero in this case means unknown due to one mass trace, yes. Thanks for clarifying. Would it work with just one mass trace (i.e. is the comparison of the...
Very nice find. I think that explains some discrepancies in our proteomics workflows as well. We had similar experiences in low signal areas. Regarding the "before the trace starts": it...
By the way, could it be that you used the same figure twice for the first example?
FFM calculates the std dev of the mass traces anyway. Why not use it for the tolerance in requantification?
Could this also be integrated into XTandemFilereader class? Because then it would be available in the XTandemAdapter and pyopenms as well. Otherwise, we create new/different workarounds every time we deal...
Hmm yes, sounds bad. Unless the analysis software uses a fixed binning approach and you can use the number of IM bins to map back. Or raise an issue at...
ProteinQuantifier will only use peptides that are unique or unique to an **indistinguishable** group (e.g. only shared by all the proteins in such a group). In the second case, it...
Yes I forgot that they have the additional protXML. I mean that. Only if the protXML converter outputs ```xml ``` their peptides will be used for quantification of the whole...
I can look at the protXML parsing but now that you are mentioning "missing in one plex" again (which I kind of ignored for now), I don't think this has...
Yes, that is correct. What I am saying is just, that this does not really affect the plex-completeness of proteins (or at least in a non-trivial way, since it depends...