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Uploading timstof files to create skyline library

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Uploading timstof files to create skyline library susmitaghosh191996  2025-04-17 03:43
 

I am currently trying to export isolation list for PRMPASEF method for which I need spectral and ion mobility library. I wanted to create that with the PEPXML file ontained from PEAKSONLINE database search. However, I am constantly getting the attached error. Therefore, it will be helpful if you guide me what to do further.
 
 
susmitaghosh191996 responded:  2025-04-17 04:00

When I tried with the raw DDA files to create the library, it kinda worked but it always shows just the precursor no transition information. When I remove p ion type from the transition settings, I cannot see anything. I have attached the skyline file for your reference.
 
Nick Shulman responded:  2025-04-17 09:41
Do you have the .mzML or .mzXML files that were used in your PEAKS search?

I believe the error that you are getting ("Could not translate integer 64638 to native id format Bruker...") is because the .pepXML file is identifying the spectra with just a single number, but, in general, it is not possible to figure out which spectrum in the raw data that actually refers to.

When you convert a Bruker .d folder to .mzML or .mzXML, a flat list of spectra is produced. However, converting from a position in that list back to the spectrum in the .d folder would require knowing the exact settings that were used to do the conversion.

You might be able to get this to work if you put your .mzML or .mzXML files into the same folder with the pepxml file. Also, make sure not to have the .d folder in there, because BiblioSpec might try to use the .d folder instead of the .mzML or .mzXML file if it finds the .d folder.
-- Nick
 
susmitaghosh191996 responded:  2025-04-23 01:06
Hi Nick,

It worked with .mzXML files. So I could create the library thanks for your help. However, I still have the problem in importing the result file. Since I used .mzXML file to create the library, I used .mzXML to import as result file. But interestingly, after 68% of file upload, it stopped uploading. I tried closing the software and retsarted again but dindot work.

Best,
Susmita
 
Nick Shulman responded:  2025-04-23 07:45
You only need to use the .mzXML for creating the .blib spectral library.
For extracting chromatograms, we would recommend that you use the .d folder instead.
Skyline will know that the spectra and retention times in the .blib file correspond to the .d folder that it is extracting chromatograms from, because Skyline recognizes that the .mzXML and .d folder have the same filename with different extensions.

It's still sounds strange that it got stuck in the middle of chromatogram extraction when you were using .mzXML files. If you would like, you could send us your files and we could try to figure out why it got stuck. You can package everything up in a .zip file and upload it here:
https://skyline.ms/files.url
-- Nick