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Failed to attempt reintegrate peaks_index 6 must be between 0 and 5

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Failed to attempt reintegrate peaks_index 6 must be between 0 and 5 vanyabangera  2024-09-10 22:45
 

Dear Team,

We are failing to train mProphet model in skyline version 22.2.0.527 (841287d47) and 24.1.0.199 (6a0775ef83). But unable to reintegrate. It's showing pop-up "failed attempting to reintegrate peaks. The index 6 must be between 0 and 5". As per the suggestion obtained from previous queries we tried to perform the rescoring but failed to reintegrate. Kindly advice to resolve the issue.

Thanks in advance.

Kind regards
Vanya K N
 
 
Nick Shulman responded:  2024-09-10 23:00
It sounds like you already found the other support request where this error was reported:
https://skyline.ms/announcements/home/support/thread.view?rowId=27885

In that other support request, the problem was that there were multiple identical peptides in the document which had different precursors under them.
I do not know whether we actually fixed the bug that was causing that error in that person's document, so it is possible that that is the problem that you are running into.

It would be most helpful if you could send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request.
You can always upload larger files here:
https://skyline.ms/files.url

After I see your Skyline document I will probably be able to figure out what is going on.
-- Nick
 
Nick Shulman responded:  2024-09-11 08:24
Thank you for uploading that Skyline document.
I am not seeing the error that you describe about an index not being in the right range.
I do see the error "Failed training the model: Insufficient target peaks (0 with 83014 decoys) detected at 2% FDR to continue training."
It appears that the decoys are not scoring any worse than the targets, which might mean that too many of your targets cannot be detected in your sample. Skyline might be able to do a better job if you reduce the set of peptides in your document to a set of peptides that are more likely to be detected.
-- Nick