Thermo raw data

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Thermo raw data cntangka37533  2025-07-08 09:19
 
Hi,
 I have recently received Thermo raw files for LC MS/MS phosphorylated sample. When the raw files are imported to Skyline to build a spectral library, +2, +3, and +4 peptides are shown. To include +1 peptides, I have tried the following: In the transition settings for product ion selection: from ion 1 to the last ion or ion 2 to the last ion but it does not seem to help getting +1 charge peptides. Is there another parameter that I could try?
Thank you,
Christiana
 
 
Nick Shulman responded:  2025-07-08 09:46
One reason that you might not be getting any +1 precursors would be if the in the "Product ion selection...From" setting on the "Filter" tab at "Settings > Transition Settings" were "m/z > precursor".
This is the default option for that setting, but it does prevent you from getting charge 1 precursors since the only way for a fragment ion to have a greater m/z than its precursor would be for the product ion to have a lower charge.
If you change that to "ion 1" or "ion 2" you might end up getting some charge 1 precursors.

Even if Skyline has not given you the precursors or transitions that you want, you can usually add them by right-clicking on the Peptide or Precursor in the Targets tree and choosing "Pick Children".

The child picker window has a filter button on the left (looks like an inverted triangle) which you might need to toggle off. After toggling off the filter button you should see all of the precursors or transitions that you want and can add them manually.

If you would like, you can send us your Skyline document and we can tell you what is going on.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick
 
cntangka37533 responded:  2025-07-08 11:31
Hi Nick,
Thank you so much for your response. Would it be possible to share the zip file privately?