Chromatography Forum

Hello,
Would be great if someone could give me a hint what can cause a vary between matrix effects on quantitative and qualitative mass transition in
LC-ESI-MS/MS. The precursor ion is the same for both transitions.
Different is bigger than 100%

If i understand your post correctly, what you're seeing is not the matrix effect in LC-ESI-MS.

While the matrix effect is a very complex process and not (yet) understood on a molecular level, there is a consensus that suppression/enhancement happens mostly during the process of going from ions in liquid to ions in the gas phase in ESI-MS. In other words, it happens before the collision process.

You see a difference in fragmentation pattern of a single precursor ion to 2 daughter ions in sample, relatively to the same precursor in solvent, right? Are you looking at a spiked or an unknown sample?