which fragment ion should be used for quantification

[jiangds06]

generally base peak, or the second largest peak?

[rb6banjo]

I usually choose one that is unique and hopefully quite larger. A unique fragment makes most of the other stuff you don't care about vanish and a large one gets you the sensitivity you want. You should also monitor some others that are characteristic to your analyte so that you don't identify a coeluter as your analyte. The ratios of the fragments should be characteristic of your analyte. Generally, even isomers have different ratios of the fragments generated.

Good luck!

[jiangds06]

make sense. thanks.

I usually choose one that is unique and hopefully quite larger. A unique fragment makes most of the other stuff you don't care about vanish and a large one gets you the sensitivity you want. You should also monitor some others that are characteristic to your analyte so that you don't identify a coeluter as your analyte. The ratios of the fragments should be characteristic of your analyte. Generally, even isomers have different ratios of the fragments generated.

Good luck!