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error when importing DIA data from a shimadzu LCMS-9030

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error when importing DIA data from a shimadzu LCMS-9030 jcaceresvergara  2023-10-31 12:03
 

I'm getting this error when I try to import DIA data from a qTOF shimadzu LCMS-9030.

I have tried to directly import the .lcd data and also transform it into mzml data.

At 12:01 PM:
Failed importing results file 'D:\JC\Shimadzudata\20231026\20231026_P450Sec_DIA_001.lcd'.
error reading spectrum scan=1

I don't see this problem with DDA data, have not tried MRM yet.

thanks a lot.
Juan Carlos.
 
 
Nick Shulman responded:  2023-10-31 12:33
I don't think we have seen that error with Shimadzu files before.
Can you send us your Skyline document ("File > Share...") and that .lcd file?
You can zip everything up and attach it to this support request if it is less than 50MB or upload here:
https://skyline.ms/files.url

One way to check whether this is just a problem with the .lcd file would be to try looking at the file using SeeMS.exe which gets installed when you install ProteoWizard.
-- Nick
 
jcaceresvergara responded:  2023-11-01 18:01
Hey Nick,

I'm sorry about this, I did not notice the isolation scheme in the transitions settings was not appropriate. I did change it and the data loaded correctly.
I changed it back to other options and was able to reproduce the error:

If in the "full scan" tab, MS/MS filtering I chose DIA with isolation scheme "results only" or "results (0.5 margin)" I get the error when I load the data into skyline. if I do DIA with isolation scheme "SWATH (15 m m/z) I can load the data properly.

thanks a lot.
Juan Carlos.
 
Nick Shulman responded:  2023-11-01 18:16
An incorrect isolation scheme is not supposed to result in an error like that.
It sounds like something else might be going on.
My guess would be that ProteoWizard is having trouble reading the data from a particular spectrum, or (if you have chosen "Centroided" as the mass analyzer at "Settings > Transition Settings > Full Scan") is having trouble centroiding that spectrum.
Your choice of isolation scheme might cause Skyline to skip over the problematic spectrum because it does not match any of the precursors in your document.

You might also run into the same error if you were to use MSConvert to convert your .lcd file to .mzML.
If you are centroiding in Skyline then you should apply the "Peak Picking" filter in MSConvert in order to reproduce what Skyline is asking ProteoWizard to do.

This sort of error might be caused by corrupted data in the .lcd file, in which case there probably would not be much that we could do about it.
-- Nick