got to quantitation mass hunter. File, new batch, add samples(blank sample, set of calibrations,samples). Then, go to method, add from aqusition one, it will bring all your MRM . After that, on the left you can see different icons that enable you to difene qualifiers, concentrations of calibrations, ...
finally on the lift also, go to internal std . Define the intstd comopund,
Note for points of caliprations of the internal standard , they all will be with same conc.
MassHunter has two different processing softwares, one for qualitative processing and the other for quantitative analysis. If you want to quantitate a set of samples in MRM, you must open the one named QQQ Quantitative Analysis and proceed, in summary, as Sheriff said, but it is not that easy. This is not an easy process, so, I recommend you to read the paper Fabian recommend. read slowly this manual and, if possible, try to follow the workflow step by step. then, you will find out your own way to quantitate a set of samples.