Adjusted P-value and CI are not being calculated for group comparison of imported Fragpipe DIA data (peptide)

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Adjusted P-value and CI are not being calculated for group comparison of imported Fragpipe DIA data (peptide) jason murphy  2026-04-02 07:58
 

I imported Fragpipe (ver24) DIA peptide results into skyline (26.1) for 3 samples with triplicates and I'm able to get the fold change when running the group comparison however the adj p-value and CI are not being calculated. I'm doing peptide level quantitation, and realize I should probably use MSstats but it would be nice to have a quick survey of the data with P-values in Skyline.
I uploaded the fragpipe.sky.zip file
thanks for your help

 
 
Nick Shulman responded:  2026-04-02 11:48
You should change the "Identity Annotation (for technical replicates)" to blank.
That is currently set to "Condition", which is the same as the "Control Group Annotation", which means that Skyline thinks that all of your samples for a particular cohort came from a single individual and so there is no way to estimate variance across the population so there is no confidence interval or p-value.

It is important to use the Identity Annotation if you have technical replicates, because there will be lower variance among your technical replicates and if Skyline did not know that they came from the same individual, Skyline would underestimate the variance in the population and you would get a better p-value and smaller confidence interval than you should.

However, if you do not have technical replicates, and each of the Replicates in your Skyline document came from a different individual then you should leave Identity Annotation blank.
-- Nick