Meaning of 'Min peak found ratio' (refine->advanced settings)

Meaning of 'Min peak found ratio' (refine->advanced settings) Emma Jappe  2019-11-08

I am analysing DIA data and have a spectral library that I am searching my DIA data against. Some of the transitions are of very poor quality (indicated with a red dot) and I would like to remove these; however, I have a lot of data and it would take a few days to do this manually. I have been looking at some of the filtering options in edit->refine->advanced and in the results tab, I have set a cut-off on the 'Min peak found ratio' to 0.8. Can you describe to me the meaning of this setting as well as the other settings (max transition peak rank etc).
Thanks a lot!

Nick Shulman responded:  2019-11-08
When you specify a peak found ratio of 0.8, transitions will be deleted from the document if a peak was not found for those transitions in at least 80% of the replicates.

What it means for a transition peak to be "found" depends on whether or not the menu item "Settings > Integrate All" is checked.

If "Integrate All" is not checked, then a peak will be considered "not found" if its apex is not within a quarter of the full peak width from the apexes of the other transitions under that precursor.
If "Integrate All" is checked, the a peak will be considered "found" unless the chromatogram is completely flat across the area being integrated.

In the Refine dialog, if you hover the mouse over the textboxes, you should see a tooltip which describes what the setting does. For "Max Transition Peak Rank", the tooltip says:
All transitions with an average area peak ranking
greater than this number will be removed from the

What that tooltip means is that for each Precursor in the document, Skyline sorts the transitions by the average transition peak area across all of the replicates. Any transitions after the Nth element in that sorted list for that precursor gets deleted from the document.

Let me know if any of the other settings are not clear. I am not sure whether we have a document anywhere that describes what all those settings do.
-- Nick
Emma Jappe responded:  2019-11-09
Hi Nick,
Thanks for the quick response! However, I don't quite understand how this can be the definition of 'min peak found ratio' as the setting doesn't remove transitions but removes entire peptides. When I change to this setting and select 'replicate inclusion' -> 'best', it seems as if all peptides (with the best result, either dotP or idotP) with <80% transitions found are removed from the document. Isn't this the meaning of the setting?
I am interested in finding a setting that allows me to remove all transitions/peaks that are not found (in a specified replicate) when 'integrate all' is NOT checked. I have tried different options in the document grid but this only allows me to delete transitions that are completely flat across the peak in the chromatogram when I filter on a specific replicate. Can you help me with this?
Thanks again,
Nick Shulman responded:  2019-11-09
If you have "Replicate Inclusion" set to "Best", then a transition's peak found ratio will always be zero or one depending on whether it was found in the "best" replicate for its peptide.

The "best" replicate for a peptide is the replicate which has the largest total area across all of the transitions under that peptide.

There is a column in the Document Grid which tells you whether a transition would be considered "not found" if "Integrate All" were not checked. That column is called "Coeluting". It's under "Proteins > Peptides > Precursors > Transitions > Transition Results". If "Coeluting" is False in the Document Grid then the transition result would be shown as red if Integrate All were not checked.

-- Nick