Library free search unknown modifications

[RobbinBouwmeester]

Dear @vdemichev,

I was checking the predicted library prior to a search and as expected some of the (unknown) modifications do not have predictions that accounts for the modification (e.g., --var-mod UniMod:1363,68.026215,K). As a result the modification is ignored. This behavior is I believe as expected.

After searching a file the outputted library does contain a value for the predicted retention time. If I am right this value is obtained from the searched data to create a new spectral library. However, this predicted retention time value can be quite different from the apex that is observed according to DIA-NN (in the single file I searched).

So I wonder if the predicted value is actually predicted with a model or that an observation from the raw file is used. If the latter is the case, how does it determine the apex? And why is there a discrepancy with the reported apex?

Thank you!

Kind regards,

Robbin