Indeed, introducing a change in the mobile phase can influence the concentration. However, in the process of quantification, it's common practice to dilute each point on the calibration curve using the same mobile phase as used for the samples. This correction ensures that the concentration remains accurate.
To provide more precise assistance, it would be beneficial if you could share the protocol you're following and describe your quantification methodology in this context.
If matrix-matched calibration exists, it is ok...If there is not, use normalization by spiking IS to compensate the differentiation...Otherwise, you should calculate the recovery and multiply the results by the method recovery for accurate quantification...