Hi Matt,

Just to make sure I understand the issue: is it that Tune no longer understands the export from Skyline, or is it that Skyline can't accept Tune output?

If the problem is in the Skyline -> Tune direction we'll have to figure out how to satisfy previous versions of Tune at the same time.

Screenshots would be welcome, so I can best understand your situation.

Thanks,

Brian

Hi Brian,

I exported an isolation list from Skyline using the Q-exactive vs. Fusion settings, and I imported these into methods on our Q-Exactive and Fusion Lumos, respectively. The QE inclusion list is as expected, but the Fusion Lumos inclusion list has lost the correct "end time". Note that export of an isolation list using the current Fusion setting does not export the peptide name (heavy or light). This would belong in the "Compound" column in the Tune 3.0 inclusion list.

Regards,

Matt

This seems like a bug in Tune's reader. Have you alerted Thermo?

That aside, I certainly prefer the new format (much better for small molecule use), and we should add an option for "Lumos (Tune 3+)" or similar to take advantage of those new fields. Can you provide information on the full range of column headers supported there?

Thanks

Brian

Hi Brian,

This is a relatively new instrument so our first experience with PRM on a Fusion or Fusion Lumos. Perhaps the export was valid for an earlier version of Tune. I exported the mass list table from tune 3.0 with all available options, which include most of the settings in the tMS2 scan.

-Matt

>> Perhaps the export was valid for an earlier version of Tune.

Just so - but the fact that it's *almost* valid for Tune 3.0 makes me think it's a reader bug that Thermo might want to know about. It seems like they meant to handle the older format but had some problem with the end time column, and it would be a kindness if a customer would alert them to it.

Anyway, onward and upward - thanks for the comprehensive list, that's very useful. We'll work on getting 3.0 compatibility implemented.

Hi Matt,
This has been implemented and will be available in the next release of Skyline-daily. It appears as a checkbox option when exporting for Thermo Fusion.

Thanks,
Kaipo

Thanks! Just tested it. Matt