Re: Issue with .cdf files
Reply #1 –
You will need to know what is in each function/scanEvent to know what is best to do. Analyzing different functions together probably doesn't make much sense. One could be a low energy scan and the other a high energy scan, or MSE.
If you open the _extern.inf file inside the raw folder each function is described at the bottom.
For conversion with proteowizard you have two problems:
1) Centroiding (if your files actually were recorded in profile mode). For waters data msconvert cannot use the Waters centroiding algorithm. It uses its own which is inferior. You can get around it by centroiding the files in masslynx to create centroided raw files that can then be converted
2) Accurate mass. It used to be that msconvert were not able to use the lockmass information to calibrate the masses. So you got uncalibrated data. Now it appears that the solution depends on how the files were recorded and the version of masslynx... So yes a big mess. Options are:
a) Some files will need the lockmassRefiner filter in msconvert. From my short tests it appears that some newer versions of masslynx will do the conversion correctly without this now.
b) Some files now seem to have the correction baked in.
You will need to check the masses masslynx is showing and comparing to the converted file to understand if things were converted correctly.