Trouble processing Orbitrap Ascend DIA files

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Trouble processing Orbitrap Ascend DIA files jason.murphy  2024-03-20 11:45
 

I have both an Orbitrap eclipse and Ascend in my lab. I have acquired DIA data on both instruments, and I have successfully processed the Orbitrap Eclipse DIA data in Skyline. However when I try to process the Orbitrap Ascend DIA files Skyline throws an error and aborts the process. The software seems to have a problem recognizing the isolation windows in the .raw file for the Ascend. Even when I manually enter the isolation windows the processing still fails.
thanks for your help

 
 
Nick Shulman responded:  2024-03-20 12:48
Can you send us one of your .raw files?
If that file is less than 50MB you can attach it to this support request but it will probably be bigger than that so you should upload it here:
https://skyline.ms/files.url

That .raw file will probably be sufficient for us to reproduce your problem, but you might also want to send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.
-- Nick
 
jason.murphy responded:  2024-03-20 13:07
Okay I just copied the file named "Ascend_DIA.raw". Do I need the thermo "msfilereader" program on my computer for skyline to process the .raw file? Although it already worked for the eclipse DIA file so I guess not

thanks
 
Nick Shulman responded:  2024-03-20 13:22
Thank you for uploading that .raw file.
I can't get anything bad to happen with it.
It might be that the behavior you are seeing has something to do with the specific settings in your Skyline document.

Can you send me 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 and spectral libraries.
If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:
https://skyline.ms/files.url

Also, can you give me more information about the error message that you are seeing?
-- Nick
 
jason.murphy responded:  2024-03-20 14:24
Title: here is the error code
Starting DIA-Umpire conversion
Error processing file C:\Users\murphja4\OneDrive - Novartis Pharma AG\Desktop\Ascend_DIA.raw

Command-line: C:\Users\murphja4\AppData\Local\Apps\2.0\RP5M7AX5.2A7\GJJ6TLRL.EXX\skyl..tion_2e441fc3bf6adc7f_0016.0002_43bc2aaae83999e5\msconvert -v --32 -z --mz5 -o "C:\Users\murphja4\AppData\Local\Temp\1" --outfile ahdbtf5j.0z2.mz5 --acceptZeroLengthSpectra --simAsSpectra --combineIonMobilitySpectra --filter "peakPicking true 1-" --filter "diaUmpire params=C:\Users\murphja4\AppData\Local\Temp\1\nwz5hn2n.umb.params" "C:\Users\murphja4\OneDrive - Novartis Pharma AG\Desktop\Ascend_DIA.raw"
Working directory:
Conversion failed.


I'm trying to upload the zip .sky file now.
 
Nick Shulman responded:  2024-03-20 17:28
Thanks for uploading your .sky.zip file.

I see that you are using Skyline version 22.2.
The latest released version of Skyline is 23.1.
Things seemed to work for me when I tried this in Skyline 23.1 and in Skyline-daily.

Is there a reason you're using such an old version of Skyline? We usually recommend that you use the latest version of Skyline unless you are trying to reproduce results from older experiments.
-- Nick
 
jason.murphy responded:  2024-03-21 10:57
Hey Nick

Thank's upgrading the software to latest version fixed the problem. Didn't even realize I was using an older version, our intranet is locked down so we are not able to easily update external software.

Thanks
Jason