Negative iRT values

Negative iRT values smanda  2020-02-02

Hi Brendan,

I am using irt calculator to in Skyline to calculate the normalized iRT values for my spectral library based on a set of 30 standard peptides. I see that in the results some of the normalizedRT values are negative. What could the reason? Any pointers?


Nick Shulman responded:  2020-02-02
Some negative iRT values are expected. Typically you would assign the value 0 as the iRT score of your earliest peptide standard that you add to your sample, and 100 to the latest eluting peptide. However, there often will exist endogenous peptides whose retention time happens to be earlier than that first standard peptide and those peptides will have a negative iRT score.

If you would like, you can send us your Skyline document and we can see whether anything looks suspicious. In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including iRT database and extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
-- Nick