Method Development Workflow for Small Molecules

Method Development Workflow for Small Molecules Richard Lam  2019-11-13


Do you have tutorials on optimizing MS/MS parameters for small molecules?
Note: I only have the precursor m/z info, fragments ions are unknown. It seems like the small molecule tutorials available in Skyline website are only for for both precursor and fragment ions are pre-determined already.



ekramh1982 responded:  2019-11-14

If you only have precursor info but want to do MS/MS, I am guessing you are running PRM? For PRM, the only other thing to optimize would be collision energy. Use the "Stepped Energy" function inside the Thermo software for that. However, to do analysis of data in skyline you have to provide product ions (or if you are doing MRM in triple quad).

This webinar might help: Webinars/Webinar 16/begin.view

Richard Lam responded:  2019-11-18

My goal is to develop MRM methods for a list of small molecules using Q-Trap.
As I mentioned earlier, I have the precursor ion information but fragments ion are not known yet.
Can I use Sciex Q-Trap to perform PRM?


ekramh1982 responded:  2019-11-18

Richard I have not used Sciex Q-Trap. However reading this :

It looks like you can do "Enhanced Product Ion (EPI)" on page 8

So yes, if you have the precursors, you can find the MS/MS for each of them and then develop your MRM. Problem is PRM as in Thermo (where you give a list of precursors and all fragments are collected) might not be available in Sciex. But you have to verify that option in the sciex software. Else, you have to collect MS/MS for each target individually.