trishorts
trishorts
because the centroiding actually gets done in mzspectrum. So, seems like once it gets centroided, the variable should be set. The scan just takes what it gets. No point setting...
can you provide an mgf file to use in our unit test?
I submitted a pull request that should solve the problem. I need two reviews to get approval for merge. then I will make a PR to MetaMorpheus w/ the update....
Can "Protein core" be any amino acid in the protein, even on the termini? I can't find a definition at uniprot. Google says that protein core is simply solvent inaccessible....
if we were to use one of these mods in a gptmd scenerio, what would the rules be?
I did an analysis of "feature type" in human canonical uniprot.xml and got the following table: 
lipid-binding is pretty far down the list (but fine). I guess, we need to look at these and decide what to do. I suspect there are other things we'd like...
this command handy for examining large file: grep "feature type=" xml.xml > ft.txt dumps every line containing "feature type=" to new text file ft.txt
recent conversation with tal fellers makes me think that if we read a "modified residue" from uniprot.xml and we don't have a matching modification that we should provide an error...