about Edit Report

about Edit Report minyg98  2021-06-14

Hi, I want to know about a few options in Edit Report.

What is 'Peptide Peak Found Ratio' and how 'RatioLightToHeavy' is calculated?


Minyeong Ji.

Nick Shulman responded:  2021-06-14
The Peptide Peak Found Ratio is the fraction of Transitions that have a good looking peak for that Peptide in that Replicate.
This is also the fraction of transitions that have a green dot next to them in the Targets tree.

The definition of "good looking peak" depends on whether the menu item "Settings > Integrate All" is checked.
When "Settings > Integrate All" is checked, a good-looking peak is any peak that is not completely flat.
When "Settings > Integrate All" is unchecked, the peak has to satisfy several more criteria including that the retention time of the apex be within 25% of a peak width of the apexes of the other transitions.
The Peptide Peak Found Ratio column is useful when you are refining an SRM method and are trying to decide which peptides are detectable and which transitions to monitor.

The column "RatioLightToHeavy" usually shows the same value as "Ratio to Standard", but that depends on exactly what you have selected for the Internal Standard Type at "Settings > Peptide Settings > Modifications". The RatioLightToHeavy column will show the ratio of sum of the peak areas for the light transitions divided by the sum of the peak areas for the heavy transitions. There is some information on how that is calculated here:

I will improve the tooltip for the "Peptide Peak Found Ratio" column so that it has more helpful information.
-- Nick
Brendan MacLean responded:  2021-06-14
I have for a long time now felt that I should have named it instead "Peptide Peak Found Proportion". It is the "ratio" of transitions "found" (i.e. with a matching peak shape) to the total number of transitions... which is also known as the "proportion" of transitions "found".

The not-found transitions are the ones with a red dot indicator on the left side. In the Targets view a red dot to the left of a peptide means that this value is < 0.5, and an orange dot means >= 0.5 and < 1.0. A green dot means this value is 1.0.

Sorry for the confusing terminology. Maybe one day we will get around to deprecating the old name and changing it to use "Proportion" instead of "Ratio".

minyg98 responded:  2021-06-14
Thank you all!!

It was a big help