Selective peak integration based on idotp

Selective peak integration based on idotp Fabian  2018-05-29

Dear all,

i would like to have the option to integrate only peaks above a certain idotp threshold.
At the moment, the option [refine_advanced_results] Min idotp: decides if a peptide is kept or not.
I would like to have the same option based on the peaks not on the peptide.

Did I miss sth. or are there workarounds (peak training model did not convinced me).

Best regards


Fabian responded:  2018-09-14

Dear skyline team,

sorry for asking again, are there any plans to incorporate such a feature?
I like skyline a lot but I really miss this feature.
There are cases in which it is preferable to have missing values instead of picking noise or false matches.
For instance in present/absent cases in noisy spectra.

There was a similar post some years ago:

Referring to this post, the value 0 is indeed critical, but why not something like #NV.

Best regards


derock j responded:  2019-03-14


I think I have the same problem. When I use the idotp refine option, ome peaks with values below the set threshold are kept and I don't understand why.

Best regards