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XCMS Online / Issue with .cdf files
I have been trying for a while now to make sense of all of the software etc. Available for use with metabolomics.
I have water .raw data run on a ULPC water synapt G2 which I converted using databridge, this gave me four files, I think one is lock spray and one is UV data...3.cdf and 4.cdf
Initially I tried using mzmine with my .raw files but it doesn't seem to like the scan filter and I have a lot to get through so moved onto my .cdf files. I have been trying to use xcms online but I am worried that the division of my mass spec info (ie. 1.cdf and 2.cdf) is meaning that I am losing information, is this concern valid?
I have seen some other threads suggesting that waters users need to go back to masslynx and make sure all their data is centrioded before they export and convert... but others suggest using proteowizard to convert .raw files to mzxml... I have tried a while ago to convert files using proteowizard but it doesn't or at least didn't seem to like waters files at the time... has this since been updated? As a return to masslynx would be a nightmare for me as I do not have a license and would need to travel to use it!
Anyways I am feeling very lost and due to the size of the files in question trying things to see if they work takes such a long time so if anyone has any suggestions it would be much appreciated. Thanks.