wiff to mzml import

wiff to mzml import Lisa Panzenboeck  2023-08-18 07:11

Dear Skyline-Team,
I have tried to convert the .wiff and .wiff2 files generated with the zenoTOF 7600 from SCIEX to mzml files using peak picking in ms convert. After the conversion it is possible to open the file in SeeMS but the import to skyline crashes with the following error message:

At 4:06 PM:
Failed importing results file 'herewasmyfilenameandpath'.
[pwiz::CLI::msdata::ReaderList::read] Invalid cvParam accession "1003293"

I'm using Skyline 64 bit 22.2.0527 with Windows 10 Enterprise.


Nick Shulman responded:  2023-08-18 07:18
I think this will work if you use Skyline-daily instead of Skyline.
You can install Skyline-daily by clicking the "Skyline-daily (beta)" button on the main Skyline page:

CV Param 1003293 is the code for "ZenoTOF 7600" which did not get added to our code base until November 2022, so Skyline version 22.2 does not understand it but the latest Skyline-daily does.
-- Nick
Lisa Panzenboeck responded:  2023-08-22 02:13
Hi Nick,
thank you for your great support. Works perfectly fine. Will you release an updated version of Skyline soon? I am always a bit cautious when it comes to using beta versions...

Lisa Panzenboeck responded:  2023-08-24 02:57
Hi Nick,
just to make sure, it should also be possible to import MRM data and have a look at the fragment transitions with skyline daily, right?
For some reason it works for me when using the wiff file in skyline but not using the mzml file in skyline daily (although I can see the MS2 transitions in SeeMS after the conversion).