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

htl responded:  2020-05-28


I have the same question. Is it possible to remove the low idotp peaks from particular replicate? "Min idotp" from Refine, Advanced remove the peptide from all replicates.


Nick Shulman responded:  2020-05-28
When you specify something for the "Min idotp" in the Refine > Advanced dialog, Skyline deletes Precursors from the document where the average Isotope Dot Product across all the replicates is lower than that value.
On the Refine Dialog, you can also choose "Best" for "Replicate Inclusion", instead of "All". In that case, Skyline only looks at Isotope Dot Product of the replicate with the largest area.

If you would like to remove the peaks that have low Isotope Dot Products, you should use the Document Grid.
Once you have all of the rows in the Document Grid selected which you want to remove, you can use the "Actions" dropdown at the top of the Document Grid.

There's a menu item on the Actions dropdown "Remove Precursor Peaks".
-- Nick