Re: Choose the best parameters to analyse UPLC-qTof data
Reply #3 –
Yes. Masswolf as I said mixes the normal scans with the lockmass scans. and msconvert doesn't calibrate the data. Databridge in theory can convert all in one batch. However they are so eager to inform you that you have several traces/functions so they make a popup for each files. And it seems to stop randomly... never the less it is the only consistently working way available at the moment.
Understanding the quality of the data only through some calculations with XCMS is over-complicating things heavily. Does your peaks tail? Do they have the usual intensity achieved on your setup? Is the lockmass intensity at at reasonable level?. Are the retention times as they should be? Is the baseline at a reasonable level? How is the mass accuracy? Some of these can definitely be assessed by some calculations. But it is way faster to just look at the chromatogram first and see if everything looks normal. You can't spot things you are not looking specifically for with a computer. Luckily a human can.
For BPI plot see:
?plotChrom