No quantification data on isotopically labelled internal standard wangn2  2023-02-06 14:05
 

Hello Skyline support team,

I have an issue when extracting MS2 fragments integration for quantification. The quantification results (showed in the "quantification" column from the "peptide ratio result" report) of my target peptides are correctly showed, but for the isotopically labelled (+8 for Lysine and +10 for Arginine) internal standards, the quantification showed "#N/A", even though the chromatogram was correctly extracted. I wonder if this is due to some settings about isotopic labelling that I've ignored.
I attached a snapshot from the "peptide ratio result" report preview. Any suggestions would be greatly appreciated!
 
 
Nick Shulman responded:  2023-02-06 15:06
Skyline never quantifies the internal standard.
It is assumed that the internal standard has been added to the samples in a known amount and you do not want Skyline to tell you what that amount is.

If you do not want Skyline to treat the heavy peptide as an internal standard then you should go to:
Settings > Peptide Settings > Modifications
and change "Internal Standard Type" to "None".
-- Nick
 
wangn2 responded:  2023-02-07 07:12
Hi Nick, changing the internal standard type solves this issue.
Thanks a lot!