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Isolation List Export for Fusion Lumos

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Isolation List Export for Fusion Lumos jalbin  2023-10-04 15:59
 

I'm sorry if this has been addressed elsewhere, but I can't find the answer. When I use Skyline to export an overlapping window DIA isolation list for Thermo Fusion, the output looks like this:

m/z z t start (min) t stop (min) Name Isolation Window (m/z)
404.433719 8.003638
412.437357 8.003638
420.440995 8.003638
etc.

I am using a Fusion Lumos, which wants a single column isolation list that looks like this in the default XCalibur 4.2.47 method:

Calculated m/z Window
400.4319-408.4355
408.4355-416.4392
416.4392-424.4428
etc.

How can I get Skyline to export an isolation list in the format that XCalibur wants?
 
 
Brian Pratt responded:  2023-10-05 11:10

I don't have a ready answer, but I'm sure the engineer working in that area of the Skyline code will be interested to know what version of Skyline you're using, and will probably be happy to see a screenshot of the settings you're using when exporting the isolation list.

I'm sure we can sort this out - thanks for using the Skyline support board!

Brian Pratt
 
jalbin responded:  2023-10-05 12:00

Thank you. I've attached screenshots of the settings I'm using under the Calculate Isolation Scheme, Edit Isolation List, Transition Settings / Full Scan, and Export Isolation List windows as well as an Excel file with what gets exported. I'm using Skyline 23.1.0.268, and Tune 3.3.2782.16.
 
Brendan MacLean responded:  2023-10-05 14:28

Hi John,
I am sorry that what Skyline is exporting doesn't appear to be the format you need. However, it is relatively simple to achieve the single-column format that you are looking for in Excel. I did this by:

  1. Opening your CSV in Excel
  2. Adding a new column to the right with the header "Calculated m/z Window"
  3. In row two add the formula =CONCAT(A2,"-",A3)
  4. Then range select to the end

Not sure why what you need is different from what Skyline produces, but sometimes it is just quicker to use another tool to close the gap and move on.

Hope this helps you create the method you are looking for.

--Brendan