Error importing files

Error importing files marbon  2021-11-07

love your work, thanks so much!

I have successfully imported >20 .raw files from a Q-Exactive HF-X Orbitrap run into skyline (doing proteomics), but a few files from this batch of samples cannot be imported, see error below. Screenshot attached, I can upload / send the problematic file(s) if that's useful.

Failed importing results file 'C:\Users\mache_000\Dropbox (Sommerlab)\Mareike Bongers\Experiments\BILP\21\20210922_MK_MWN_70min_15cm_Mareike_SD4.raw'.
error reading spectrum controllerType=0 controllerNumber=1 scan=33698

I'm using Skyline (64-bit). I'm not a super experienced user so a "as-simple-as-possible" explanation of what I could try or do would be awesome! :)

Thank you! Mareike

Nick Shulman responded:  2021-11-07
If you click that "More info" checkbox at the bottom of the "Importing Results..." window, it will give you a little more information about the error.

I think often that error means that the raw file is corrupted, and the only thing that you can do to work around it is to use msconvert to create a mzML file which is missing the scans that we are unable to read. Sometimes that "More info" button reveals that the error is something completely different. Let us know what it says when you push the More info button.

If you would like you can send us your Skyline document and raw file.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing extracted chromatograms.
The .zip file will not contain your .raw files, so you should also send us that file "20210922_MK_MWN_70min_15cm_Mareike_SD4.raw".

Files which are less than 50MB can be attached to this support request. You can upload larger files here:

I will also send you an email in case you would like to send us your files in a more private way.
-- Nick
Nick Shulman responded:  2021-11-07
Thanks for sending me your files in email. I see your Skyline document on DropBox, but I do not see any .raw files up there.

Your email said that the error that you are seeing is:
 [RawFileThreadImpl::getMassList()] Object reference not set to an instance of an object.

That error looks similar to this one that was discussed on the ProteoWizard support board last year:

It is also similar to this issue that was reported two years ago on the Skyline support board:

I am not sure whether your issue is the same as these others, but we will probably be able to give you more information after we see your .raw file.
-- Nick