Hello! I am dealing with some tmt-label peptide data. I am setting tmt labeling of the n-terminus and K as variable modifications because I would like to be able to calculate labeling efficiency, but when I do so the auto-tune always finds a low number of PSMs with 1% FDR and the optimization is aborted. This is similar to if I just left the tmt modification out entirely. But when the n-terminus tmt label is set to fixed everything goes fine.
This runs fine:
-at -fmods 229.1629@[
This does not:
-at -vmods 229.1629@[
And obviously neither does this:
So I have a question regarding how the auto-tune is working. Is the first stage done with all the variable modifications turned off? This would seem to cause the problem I am seeing, when the variable modification is more on the fixed side of things.
If this is the case, is it possible to have a switch to "turn on" the n-terminus modification during the auto-tune?