Offset windows in DIA analysis | sweaver4 | 2023-07-31 07:44 | |||||||||||||||||||||
Hello, I'm looking through some DIA bottom-up proteomics data acquired on a timsTOF where the isolation windows were 24 m/z, but offset (i.e. 400, 424, 448... 412, 436...). How should I setup the transition settings to reflect this? I can point the isolation scheme to the .d file which successfully pulls in the m/z values used for the windows. Should I set the Deconvolution to overlap in this window? My goal is to look at the chromatograms and have the intensity traces for each fragment ion reflect only MS2 signal that was present in spectra where the precursor isolation windows were appropriate. (So if an example precursor ion was 430 m/z, fragments would show up in isolation windows 424-448 and 412-436, but not 400-424). Is this how the chromatogram extraction is automatically designed, or do I have to perform additional deconvolution before uploading my .d files? Thanks very much for any help, and let me know if I can clarify anything! I looked through the tutorials and documentation and couldn't find any specific examples for this, but apologies if it is somewhere and I missed it. Simon Weaver. |
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