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Importing peak bounderies

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Importing peak bounderies evy timmerman  2024-01-05 05:18
 

I always get the following error:
'index_outside_the bounds of the array_import_peak_bounderies'

Could you please check out for me how i can fix this? Or can this be simplified? The goal is to get the peak picking from DIA-NN instead of skyline and perform mProphet on the data set....

A 'stronger' computer also failed.
On the other hand only importing a small subset works.
This is a dataset with 18 raw files and >200,000 precursors.

Kind regards,
Evy

skyline file could not be saved to share, also there the daily version gave an error.
 
 
Nick Shulman responded:  2024-01-05 05:28
An error message like "Index was outside the bounds of the array" is an indication of a bug in Skyline.
It is possible that there is also something wrong with your .csv file, such as maybe one row has fewer columns in it than all of the other rows, but, it's certainly a bug that Skyline is not giving you a helpful error message telling you which line it is choking on.

Error message boxes in Skyline all have a copy button in the lower left corner. The copy button will copy the entire text of the error message plus everything that you would see if you were to press the "More Info" button.
If you could send us the entire text that you get when you push that copy button, we could probably tell you exactly what sort of thing Skyline is choking on.

It might also be helpful if you could send us your .csv file as well as 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 and/or your .csv file is less than 50MB you can attach them to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick
 
Nick Shulman responded:  2024-01-05 13:39
Thank you for uploading your Skyline document and 1.7 million line .csv file.

I can tell you that the first peptide that Skyline is choking on is "(UniMod:1)MAPGQLALFSVSDK" which is on around line a million.
I think the problem is that Skyline cannot handle a modification which appears before the first amino acid. If you have a modification on the N-terminus of a peptide sequence, usually, in Skyline, you should pretend that the modification is on the first amino acid. That is, it would probably work if you changed this to "M(UniMod:1)APGQLALFSVSDK".

Thank you for reporting this bug. I will try to fix it.

I am sorry that it takes so long for Skyline to import this peak boundaries file. It seems like it would take about four hours to import that entire .csv file. Most of the time that Skyline spends is reading the chromatogram data from the .skyd file.
I don't think we ever anticipated that someone would try to import such a large peak boundaries file.
-- Nick