by
sassman » Mon Mar 03, 2008 8:59 pm
First of all, use the highest purity solvents for your mobile phase. LC/MS grade solvents are highly recommended. Also be sure you have cleaned the spray plate. You may also want to clean Q0 if you suspect contamination, or schedule a service call to have the instrument cleaned. This should help with your high baseline.
To find the MRM transitions for your compound, you should use a syringe pump to infuse a high concentration (~10mg/L) of your compound into the MS. First run Q1 scan to see what the precursor mass is, and then run a product ion scan to see what the product ion is. This is also a good way to optimize your MS parameters (DF, FP, EP, etc.) as you continuously infuse the sample into the MS. You might also want to infuse the sample into a tee with the mobile phase so that your sample is in the actual mobile phase that you will be running in. This is especially important for the source dependent parameters (IS voltage, gas flows, etc). Good luck!