I am trying to use MS-DIAL to analyze MS/MS files from a Waters Xevo QQQ instrument, and having difficulties converting the files. I am able to use the software perfectly fine with my Agilent .d files, but the converted .raw files always yield the same error message: No peaks detected. Check polarity settings. Despite the files being converted to .abf, they are not properly being read by MS-DIAL. From what I've seen online and in other posts, I believe the files might be converted incorrectly (they are below 9KB). I have tried converting them to mzML files as well, with the same result. Has anyone else had this issue before?
I am not sure if this is a rudimentary question (I have just started using MS-DIAL for pollen lipidomic studies), but can anyone help to explain what the "peak spots" drag bar essentially means? I understand that 100% shows all of the suspected peaks, but as I show less and less (such as 50% or 5%), how does the program choose which peaks to show and which to remove? I thought it may be based on the intensity of the peak or the match score, but it does not seem to follow these parameters. Any advice would be appreciated!
