System that automates analysis of mass spectrometry data for oligonucleotides to generate pharmacokinetic parameters and models. A user inputs an oligonucleotide sequence and a maximum number of nucleotides that may be lost during metabolism while retaining therapeutic effectiveness. The system calculates the possible active metabolites and develops a mass spectrum filter for the mass-to-charge ratio of ions for these metabolites. Full-scan spectra are analyzed to calculate the total concentration of these active molecules present in a time series of samples. Pharmacokinetic models and parameters are calculated from the time series of total concentration. Because full-scan spectra are captured, assumptions may be modified and analyses may be quickly rerun without collecting additional data. Overall pharmacokinetic analysis is therefore much more streamlined and efficient, reducing cost, delay, and the need for a mass spectrometrist who is highly skilled in spectral analysis.