#N/A values for Normalised Area in Calibration curve grid sa825  2022-01-10 18:13
 

Hi Skyline,

Happy New Year!

I am viewing some results and I keep getting #N/A values in for Normalised Area in the Calibration curve grid.

I don't understand why? as Skyline can clearly see all 3 transitions (As shown in the image attached) but I keep getting that error?

The image shows 3 replicates of a peptide called : "GWVTDGFSSLK" and you can see all 3 transitions of the peptide detected at each replicate but as highlighted in blue, replicates 1 (31L_1) and 2 (31L_2) are showing #N/A values.

Is there a way I can fix this or is there something I am doing wrong?

Thanks,
Shimon
 
 
Nick Shulman responded:  2022-01-10 18:20
When the boundary of a peak is the same as the end of a chromatogram, Skyline considers the peak to be "truncated" and its area cannot be trusted, since an unknown amount of the peak has been cut off. If there are any truncated peaks, then the Normalized Area ends up being #N/A.

One thing that you can do is manually adjust the peak boundaries so that they are not at the edge of the chromatogram.

If these chromatograms were extracted from full spectrum data, then you might be able to make the chromatograms longer by changing the "Retention Time Filtering" settings at:
Settings > Transition Settings > Full Scan
and then reimporting.

If these chromatograms came from SRM then it would be a good idea to change your acquisition method so that the data for these peptides is acquired over a longer time range so that the peaks do not get truncated like this.
-- Nick