Peak selection

Peak selection ss  2023-05-23 01:50:05

Hello Skyline team,

I'm monitoring a peptide that elutes as a double peak (see attached), likely due to differing oxygen orientations of oxdised Methione.

I would like to obtain separate XICs for each of the peaks since to use as reporters for column performance.

Is there a way to do this in an automated manner without manual peak integration? Data is uplaoded via AutoQC and would like to avoid operator intervention.

The transitions are identical but since data is generated on a TIMS perhaps CCS can be applied as an additional filter. I'm not sure if can do this and also how to execute it in Skyline:


Brian Pratt responded:  2023-05-23 12:47:02

You'd need to add a copy of that peptide, then give each copy a different CCS value.

To do that:

  • In Settings > Transition Settings > Ion Mobility, check the "Use spectral library ion mobility values when present" box
  • In the Targets tree, Copy and Paste the peptide of interest
  • Open the Document Grid,
  • select the "Precursors" report
  • customize it to contain a "Explicit Collisional Cross Section" column
  • then set a CCS for the copied peptide and reimport the data.

I think this will work, I'd be happy to verify if I can get the raw data.

BTW the Skyline support board is a better place for this kind of question, the Skyline dev team doesn't monitor the Panorama board.

Best Regards,

Brian Pratt

sstoychev5114 responded:  2023-05-24 15:00:34

Thanks Brian, much appreciated, will let you know how this goes