Hello,
I am using XCMS to analyze a GCMS dataset with unit mz resolution and basing my parameter values on the "GC/Single Quad (matchedFilter)" values of XCMSOnline. Based on my understanding of the parameters, I modified "step" to match the instrument resolution ( step =1 in my case), but I am not sure how mzdiff and mzwid should change instrument resolution. I thought they should each be > "step" value, but in the default parameter set "step" = "mzwid" (both are 0.25).
Any clarification of how instrument resolution impacts selection of mzdiff and mzwid values would be appreciated.
R version 3.1.0
xcms version 1.40.0
Thank you,
Caroline