1. A method of generating an inclusion list for targeted mass spectrometric analysis, comprising: a. receiving, at a computer, experimentally-acquired data for a plurality of isobarically-labeled peptides of interest, the data including, for each one of the isobarically-labeled peptides, a mass-to-charge ratio (m/z), a charge state, and a chromatographic retention time; b. determining, via the computer, for each one of the isobarically-labeled peptides, predicted properties for a corresponding unlabeled peptide, the predicted properties including a predicted m/z, a predicted charge state, and a predicted chromatographic retention time; and c. storing the predicted properties for each corresponding unlabeled peptide to the inclusion list; wherein the predicted chromatographic retention time for the corresponding unlabeled peptide is determined based on hydrophobicity indices of the isobarically-labeled peptide and the corresponding unlabeled peptide, and chromatographic conditions for the targeted mass spectrometric analysis.