Dear skyline Team and users,
Is there a way to tell Skyline to import only FTMS MS2 Scans from a raw file? I'm running a Orbitrap Fusion method that triggers MS2 scans in both the Ion Trap and the Orbitrap. Obviously, I want the MS2 fragment trace extraction only from the FTMS scans, but I can't find a setting for this. I set the "Transition" setting to "Targeted", "Orbitrap" with "15k res" at "200 m/z".
In the attached image is the result of the current trace extraction, have I missed a setting?
I'm running Skyline 3.6.0 on a Win7 system.
Thank you very much,
Cheers
Daniel |
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| Brendan MacLean responded: |
2016-12-21 11:28 |
Hi Daniel,
Thanks for reporting this. It is just something we never planned for. I have contacted you in the hope of getting example files that would allow us to implement a solution and test it with your data.
--Brendan |
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| danielz responded: |
2017-06-28 04:49 |
Hi Skyline Team,
is the implementation of such a filter planned for the future? Otherwise i'll will take the reroute of converting and filtering my RAW files to MFG etc.
Best
Daniel |
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| Matt Chambers responded: |
2017-06-28 07:36 |
Hi Daniel,
Msconvert can easily filter spectra based on mass analyzer. Unfortunately it's only supported in the command-line tool right now - the GUI supports filtering by activation type but not mass analyzer. Here's the command-line (we recommend mzML output because it preserves nativeIDs and metadata much better than MGF):
msconvert.exe data.RAW --mzML -v -z --filter "analyzer <analyzer name>"
Where <analyzer name> is one of:
quad
orbi
FT
IT
TOF
Hope this helps,
-Matt |
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| Brendan MacLean responded: |
2017-07-01 06:30 |
This is definitely your immediate path forward. I imagine you could also do this with MSConvertGUI, if you are more comfortable with that than the command-line option Matt presented.
We will also consider imposing such filtering based on the settings in Skyline, i.e. not allowing IT spectra to be filtered when the settings indicate high resolution filtering.
Thanks for posting your use case to the Skyline support board.
--Brendan |
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