surequant MS/MS peak extraction fails

surequant MS/MS peak extraction fails 15702446287  2023-08-16 02:29

Hello skyline team´╝î
We use the Exploris systems to acquire tPx data using the SureQuant method. We can see the target peptide (light and heavy) using xcalibur software, skyline also can extract the heavy peptide , but the light peptide detection fails. for more details please see the attachment.

Is this a known issue and is there a solution for this?

Many thanks!


15702446287 responded:  2023-08-16 02:34
Nick Shulman responded:  2023-08-16 07:45
The reason that the light chromatogram is not showing up is that the "Explicit Retention Time" on the peptide has been set to "21.73", but the extracted chromatogram does not overlap with that time.
When a peptide has an Explicit Retention Time, Skyline always discards extracted chromatograms which do not overlap with the Explicit Retention Time.

You should change the Explicit Retention Time of that peptide to blank.
After you blank out the Explicit Retention Time, you can use the "Reimport" button on "Edit > Manage Results", and then chromatograms will show up for that peptide.
-- Nick