Comparison of MS-DIAL Versions for UHPLC-MS/MS Analysis

June 14, 2023, 05:37:15 AM

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?

Re: Comparison of MS-DIAL Versions for UHPLC-MS/MS Analysis

Reply #1 – June 24, 2023, 08:29:19 AM

1. 4.9 is more stable, so please use it for all LCMS/MS analyses.
2. Should show
3.In the LC world, one cannot compare RTs unless you used the same identical LC Column, buffers/ solvents, and flow rates among other LC variables that of the reported reference library/ spectra. You got to live with matching MS1 (accuracy) and MS/MS spectral matches. RT can only be indicative, for example, if a match is polar or non-polar and if the elution makes sense. If you generate your own MS/MS library in house using your own methods then RT matches can come into picture.

Alternatively check "Retip" for prediction of RT and use it as a filter OR converting RTs into RIs.

Hope this helps.