We are using Agilent 6560 IM-QTOF to run some standard compounds to generate in-house library.
After using MS-Dial to extract peak information, a lot of compounds have a big mass shift which is around 20 ppm (the mass accuracy in raw file (.d) is less than 5 ppm). We have tried different importing methods, including directly drag and drop it into the MSDial or convert it to ibf file first, but both methods give us the same problem (mass shift). I am wondering if anyone also has the same problem and how you address it.
I have a question about using MSDial to analyze the Agilent 6560 ion mobility AIF data. For example, in attached picture 1, when I select chromatography as the separation type, "SWATH-MS" and "All ion with multiple CES" option are available in the MS Method type.
However, in attached picture 2, when I select the "Ion mobility" in the separation type, there is no option about "all ion with multiple CES"
Thus, I am wondering how to use the MSDial to analyze the data which run under ion mobility and AIF using Agilent 6560.
