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.
Thanks in advance.
Most likely the problem is coming from "alignment" of all ran files/ compounds together!
Its a forced alignment error for RT and m/z dimensions both thats resulting in this mass shift and also RT shift that you can see.
Only trick, laborious one: Do it one by one on MS-DIAL. Do not run them all together or align!
If not, then learn to live with that mass-shift which does not affect MS/MS similarity matching or even MS1 based matching as it does not affect much, plus you got RT dimension to give you confidence.
Hope it helps!