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XCMS / Lockmass gap correction
I have a question regarding the correction of the gaps caused by lockmass scans.
I´m working with waters Masslynx files that I've converted to netCDF format using the Databridge software from Waters.
When setting “ lockMassFreq=TRUE” in xcmsSet I got an error message for some of the files of my dataset. Going back to those chromatograms I realised there was a problem during lockmass acquisition: it seems that occasionally the sampling baffle failed to rotate to the correct sample/reference position so that a reference scan was taken when a sample scan should have been taken (or vice versa). As a result, the lockmass scans do not adjust to a fix frequency in those chromatograms.
I wonder if there is any way of correcting those gaps other than using the lockmass frequency (for example using the lockmass data file?)
Thanks,