I am processing waters .RAW data acquired on a Synapt G2-Si with the ABF converter and then through MSDIAL. Unfortunately I have had trouble getting reasonable processing times. The acquisition is an 11 minute positive mode MSE/DIA method, the RAW and ABF files are ~5 gb unfortunately which I think is part of the issue. I have 105 files which I have tried processing with different numbers of threads. With two threads 25-40 GB RAM are used. With any large number of files (~30) MS-DIAL will frequently crash before completion. If more than one adduct is selected this problem is greatly exacerbated.
Does anyone have suggestions on how to ease the computational load or solve this problem?
Hi,
First, MS-DIAL now supports direct processing of the .RAW files without the need of prior conversion to .abf. Besides, do you mean each file is ~5 GB big or the total size of all your files? In the former case, I would guess that you have profile files? then the solution could be that centroid the file first using for example Masslynx.
Best,
Qizhi Su
Thank you, I did see that .RAW is an option in the import dialog however when I attempted to import the .RAW files they opened as folders instead of being read as files. Is there some kind of setting that needs to be changed for these to be seen as data files? I am on Windows.
Yes, each file is 5 gb, ~500 GB between all files. I will attempt to centroid the files in Masslynx, I didn't know this was an option but found Waters' documentation on it.
Thank you for the assistance.
to read .RAW files, you have to "drag and drop" the files but not open them.
Maybe you can find some clues for centroiding .RAW files here.
https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion_waters/
Best,
Qizhi Su