Sorry for my late response. I was already using the last xcms version (1.34) setting the lockMassFreq=TRUE, but for some reason it does not work with my files. I was getting the same warning message whether I had the xx02.CDF files in the folder or not.
Warning in AutoLockMass(lcraw) : Lock mass frequency wasn't detected correctly
Ok, so I may be mistaken then on what databridge conversion does? I Know the lockmass scans are not included in my datafile after databridge conversion to netCDF, but I assumed that the gaps would still be there... What I wanted to do was to use the gap filling function developed by P. Benton and see if it results in an improvement in peak picking / peak quantitation.
Hi, 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,
