| Importing timstof PASEF small molecule data results in an instant Skyline crash | Chris Ashwood | 2025-07-24 05:32 | |||||||||||||||||||||
Dear Skyline team, I hope you're doing well. I'm collaborating with a group that has a timstof Pro 2 and has generated PASEF small molecule data (in negative mode). When I try to import the raw files (.d folders) into Skyline daily (25.1.1.174) , they cause an instant crash with no errors or pop ups recorded. Ion mobility is not enabled in Skyline when I do this import. If I convert the .d files (~150-300 MB) to mzML with the most recent proteowizard/msconvert version (3.0.2501) and no additional flags, conversion is successful and the mzml files (20+ GB each) import fine into Skyline (aside from the 10+ min import), as well as allowing ion mobility dimension analysis. Possibly related, if I use the "combine ion mobility scans" flag in msconvert, it crashes and isn't successful at writing a complete mzML when writing the chromatogram aspect of the mzml. I'm unable to share the data on the public server but can email a file directly, as well as any additional details needed. Cheers, |
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