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Brian Pratt responded: |
2020-05-07 08:57 |
Hi Dawn,
To answer your first two questions:
It's important to understand that Skyline is for targeted mass spec - the working assumption is that you have some idea of what was in the sample, probably as the result of using some kind of search software.
That said, you can easily use a spectral library to create a target list in Skyline, then refine your results to discard targets that clearly don't match the imported mass spec data. It's obviously a less sophisticated kind of search, but it sounds like you're comfortable with that.
Best Regards,
Brian Pratt
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dawn dufield responded: |
2020-05-18 10:28 |
how about #3? I seem many times to have to manually update each file
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Kaipo Tamura responded: |
2020-05-18 10:53 |
Hi Dawn,
This is something that is on our to-do list, but not yet implemented in Skyline.
Thanks,
Kaipo
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dawn dufield responded: |
2020-05-18 11:10 |
So there is currently no way to set a RT window and have it pick within that window?
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Brian Pratt responded: |
2020-05-18 11:37 |
Hi Dawn,
You can set an explict RT and RT window for each transition in the document grid (you'll want to reimport the data after you do). For small molecule data you can specify this directly in an imported transition list.
Best regards,
Brian
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Brian Pratt responded: |
2020-05-18 12:44 |
Hi Dawn,
I misspoke - RT is of course a per-peptide/molecule property, not per-transition.
Best,
Brian
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Brian Pratt responded: |
2020-05-18 14:58 |
Oh, and one more note - we recently made a change to how Explicit RT and Explicit RT Window work:
Formerly Skyline would use the Explicit RT information to choose the best peak within the provided RT window, and if no peak was found Skyline would pick the nearest peak even though it wasn't in the window, which was a surprise to most Skyline users. Now if no reasonable peak is found in the window Skyline simply doesn't pick a peak at all. So, you probably want to use Skyline-Daily.
Best,
Brian
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