Fraction of MS/MS data appearing on MS-DIAL

[Mitchell-McInerney]

Hi there,

I acqured 40 injections on a Thermo Q-exactive orbitrap and now when I import the dataset to MS-DIAL only a small fraction of the MS1 and MS2 spectra actually make it into the software. When perusing raw data in Freestyle, I can see plenty of peaks that I'd like to follow up on but they're just not showing up in MS-DIAL. I have used this instrument in MS-DIAL many times successfully before. One change on this occasion was using inclusion and exclusion lists to get higher quality data, but I woudln't have thought that this would make a difference. Setting the amplitude as low as 1000 doesn't change the MS-DIAL data visibility at all. I don't understand why this is happening, any help or suggestions would be appreciated!

Thanks, Mitch