Zeno wiff vs wiff2 and Skyline AutoQC import

Zeno wiff vs wiff2 and Skyline AutoQC import ss  2023-04-18 05:21:07

Hi Skyline team,

I'm importing Zeno SWATH data into Skyline using AutoQC. For each run there are a wiff and wiff2 raw files generated that seem to contain the same data when extracted in Skyline (although wiff2 files are bigger in size). Is there a preference for which file format should be processed in Skyline?

Thanks for your feedback.

Matt Chambers responded:  2023-04-18 06:42:22

Short answer: use WIFF1.

Long answer: The WIFF2 reader Sciex provided to us doesn't support extracting MRM chromatograms directly. Other than that there isn't a big difference between the two as of February when we last updated the WIFF2 reader. The last update added support for reading WIFF2s from instruments other than the X500.

ss responded:  2023-04-18 07:15:06

Thanks Matt

ss responded:  2023-04-18 07:17:27

The challenge is how to prevent AutoQC from selecting only wiff?

Vagisha Sharma responded:  2023-04-18 11:32:30

AutoQC Loader recognizes only the .wiff extension for SCIEX data. So in a folder with both .wiff and .wiff2 files it will only import .wiff. We will have to add support for .wiff2, as well as an option to select the format that should be imported. Perhaps add a "SCIEX - WIFF2" option to the "Instrument type" drop-down. I will let you know when that is available. Until then I hope that the .wiff files have everything you need. It sounds like it might even be slightly preferred over .wiff2. The bulk of the data is in the .wiff.scan files which is used by both formats.