A method of generating an inclusion list for targeted mass spectrometric analysis, comprising: receiving experimentally-acquired data for a plurality of isobarically-labeled peptides, 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, wherein each of the isobarically-labeled peptides is derived by proteolytic digestion of a corresponding protein; for each one of the isobarically-labeled peptides, performing steps, via a data processing system, of: determining a hydrophobicity index of an unlabeled peptide corresponding to the isobarically-labeled peptide; if the determined HI is less than a threshold value, selecting a substitute unlabeled peptide in accordance with predetermined criteria, the substitute unlabeled peptide being derivable by proteolytic digestion of the protein from which the isobarically-labeled peptide is derived, determining and storing on the inclusion list predicted properties for the substitute unlabeled peptide, the predicted properties including a predicted m/z, a predicted charge state, and a predicted chromatographic retention time, wherein the predicted chromatographic retention time is based on an HI of the substitute unlabeled peptide and chromatographic conditions for the targeted analysis; and if the determined HI for the unlabeled peptide is at least as great as the threshold value, determining and storing on the inclusion list predicted properties for the unlabeled peptide, the predicted properties including a predicted m/z, a predicted charge state, and a predicted chromatographic retention time, wherein the predicted chromatographic retention time is based on the determined HI of the unlabeled peptide and chromatographic conditions for the targeted analysis. receiving experimentally-acquired data for a plurality of isobarically-labeled peptides, 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, wherein each of the isobarically-labeled peptides is derived by proteolytic digestion of a corresponding protein; for each one of the isobarically-labeled peptides, performing steps, via a data processing system, of: determining a hydrophobicity index of an unlabeled peptide corresponding to the isobarically-labeled peptide; if the determined HI is less than a threshold value, selecting a substitute unlabeled peptide in accordance with predetermined criteria, the substitute unlabeled peptide being derivable by proteolytic digestion of the protein from which the isobarically-labeled peptide is derived, determining and storing on the inclusion list predicted properties for the substitute unlabeled peptide, the predicted properties including a predicted m/z, a predicted charge state, and a predicted chromatographic retention time, wherein the predicted chromatographic retention time is based on an HI of the substitute unlabeled peptide and chromatographic conditions for the targeted analysis; and if the determined HI for the unlabeled peptide is at least as great as the threshold value, determining and storing on the inclusion list predicted properties for the unlabeled peptide, the predicted properties including a predicted m/z, a predicted charge state, and a predicted chromatographic retention time, wherein the predicted chromatographic retention time is based on the determined HI of the unlabeled peptide and chromatographic conditions for the targeted analysis. determining a hydrophobicity index of an unlabeled peptide corresponding to the isobarically-labeled peptide; if the determined HI is less than a threshold value, selecting a substitute unlabeled peptide in accordance with predetermined criteria, the substitute unlabeled peptide being derivable by proteolytic digestion of the protein from which the isobarically-labeled peptide is derived, determining and storing on the inclusion list predicted properties for the substitute unlabeled peptide, the predicted properties including a predicted m/z, a predicted charge state, and a predicted chromatographic retention time, wherein the predicted chromatographic retention time is based on an HI of the substitute unlabeled peptide and chromatographic conditions for the targeted analysis; and if the determined HI for the unlabeled peptide is at least as great as the threshold value, determining and storing on the inclusion list predicted properties for the unlabeled peptide, the predicted properties including a predicted m/z, a predicted charge state, and a predicted chromatographic retention time, wherein the predicted chromatographic retention time is based on the determined HI of the unlabeled peptide and chromatographic conditions for the targeted analysis.