I have installed two versions of MS-DIAL, V.4.9 and V.5.1. I have noticed that when running V.5.1, the retention times (RT) of my compounds do not match the reference RT, and there are instances where compounds with the same m/z do not align in RT. However, when using V.4.9, some of my compounds' RT can be matched to the reference RT. I have several questions regarding this:
1. Which version is more suitable for UHPLC-MS/MS analysis? 2. Why does version 5.1 not provide RT matches to the reference? 3. I am curious if the parameters we used during the HPLC run are different from those of the reference. In such cases, how can we select compounds that match both RT and m/z from the reference?