Skip to main content ↑ ↓
Topic: mzdiff and mzwid values for low resolution GCMS data (Read 4755 times) previous topic - next topic

mzdiff and mzwid values for low resolution GCMS data

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