raw file import error : Expected sorted data

raw file import error : Expected sorted data vbuser  2023-08-14 05:26

Hello guys,

we are pretty new in using Skyline. We have problems importing .raw files which are working completely fine in the Freestyle software from Thermo Fisher.
When importing the files into Skyline we got the error that the data could not be imported due to the error: "Expected sorted data".
The other .raw files from the same experiments are can be imported completely fine.
We added one of the files to this message.

Maybe you can help us, we would be really grateful.

Thank you


Nick Shulman responded:  2023-08-14 07:12
It does not appear that there is anything wrong with your .raw file, but it does sound like you are running into a bug in Skyline.
It would be very 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 upload larger files here:
-- Nick
Nick Shulman responded:  2023-08-14 08:57
Actually, I do see a problem with the .raw file.
The retention time of spectrum #2141 is 12.356855 minutes, but the retention time of spectrum #2142 is 12.143614 minutes.
One thing that you could do is use ProteoWizard MSConvert.exe to create a .mzML file which has all of the spectra in an order which will not cause problems for Skyline.

The commandline to have msconvert.exe do that would be:
msconvert.exe --filter sortByScanTime 027-IC-dil2-1.raw

I do not know why your .raw file would have spectra out of order like this.
-- Nick
vbuser responded:  2023-08-15 03:13
Hello Nick,

we tried your solution and it worked perfectly.
Thank you very much for your help and your fast response :=