Are all peptides incl. iRTs used for normalization? roberthardt  2022-05-31 09:16:19

Dear Skyline-team,

I am just curious to know if Skyline actually uses all peptides/precursors present in the document when I select "normalize medians" in the quantification settings? Or does it only use the target peptides and omits the iRTs? I am asking because I currently rely on the CiRt peptides, of which not all are present in all my samples at the same amounts. Thus taking also this peptides into account for normalization could potentially skew my results.



Brendan MacLean responded:  2022-05-31 09:26:03

This seems like question better posted to the Skyline support board. Could you please repost it there?

roberthardt responded:  2022-05-31 09:28:38


Wrong forum indeed.

Thanks for pointing that out Brendan.