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Wiff2 files of MS/MS data from SciexOS

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Wiff2 files of MS/MS data from SciexOS jeroen kooistra  2024-12-06 01:30
 

Dear Skyline team,

Two years ago a former colleague of mine posted a question titled: "Sciex TripleQuad7500 .Wiff2 support" (roosso 2022-07-05 22:41).
We still encounter this problem, also with the newest Skyline versions.
Some methods only generate ".wiff2" files. We think this happens when we apply experiment scheduling (3.5min of ESI- followed by 3.5 min ESI+)
On import of the .wiff2 file in Skyline we get the error below:

"Failed importing results file ...
The sample .... contains no usable data."

This also happens for methods where both the .wiff and .wiff2 files are generated and we try to import the wiff2 file.
I attached a Skyline file which we use for our 'System Suitability Test', including some raw data we would like to import. The .wiff file succeeds, the wiff2 file fails to import.

The last two years we used work arounds, so that SciexOS would generate .wiff files.
At moment we develop a method which requires experiment scheduling, and so will only generate .wiff2 files.
Could you please advise how to import wiff2 files?

Thanks a lot!

Regards,

Jeroen Kooistra
 
 
Brian Pratt responded:  2024-12-09 10:22

Hi Jeroen,

I think the problem is that the reader that Sciex provides for Skyline (and msconvert, and SeeMS) doesn't want to read that file.

Opening it in SeeMS I get this message:
WARNING: the WIFF2 reader does not support SIM/MRM chromatograms or spectra; point at the WIFF file instead

The .wiff file, as expected, opens just fine.

Perhaps another Skyline developer can comment on the status of any potential updates from Sciex.

Thanks for using the Skyline support board,

Brian Pratt
 
jeroen kooistra responded:  2024-12-10 03:57

Thanks Brian.
If such an upgrade would be made, that would be great. If there are any updates, we would be pleased to hear about that.

Thanks and regards,

Jeroen