Spectral library with .ssl format for wiff2

Spectral library with .ssl format for wiff2 Thierry Schmidlin  2024-01-22 06:58

Hi all

We are trying to generate spectral libraries for skyline based on standard compounds measured in IDA mode on a Sciex ZenoTOF 7600 (generating .wiff and .wiff2 files). In this process we use Sciex OS to help annotating spectra. We would now like to implement these semi-manually annotated spectra into a library within Skyline.
In a similar approach based on Orbitrap instruments we previously successfully used the .ssl format and a conversion of the .raw file to .mzML in order to build spectral libraries in Skyline (shown in screenshot "raw ssl.png"). A similar approach using a .ssl file with ZenoTOF .wiff2 files converted to .mzML files (shown in screenshot "wiff ssl.png") resulted in an error message regarding the scan number ("Error sciex.png"). There seems to be an issue with the "native id format" used in .wiff/.wiff2 - however, the use of .ssl files seems to completely rely on the scan column being present and populated. Is there any advice known, on how to successfully link specific ZenoTOF MS/MS spectra within a run to particular compounds when builing spectral libraries in Skyline?

Thanks a lot for any help on this issue and kind regards


Brian Pratt responded:  2024-01-22 08:11

Hi Thierry,

Have a look at the mzML to understand how WIFF scans are described - it's not a simple integer. Once you modify your .ssl writer to output that format it should all be fine.

Best regards,

Brian Pratt