Abstract: A method of generating an inclusion list for targeted mass spectrometric analysis is disclosed. Experimentally-acquired data for a plurality of isobarically-labeled peptides derived by proteolytic digestion of a corresponding protein. The data includes, for each of the isobarically-labeled peptides, a mass-to-charge (m/z) ratio, a charge state, and a chromatographic retention time (RT). The method includes determining a hydrophobicity index (HI) of an unlabeled peptide corresponding to the isobarically-labeled peptide. If the determined HI is less than a threshold value, a substitute unlabeled peptide is selected in accordance with predetermined criteria and predicted properties for the substitute peptide are determined and stored on an inclusion list. If the determined HI for the unlabeled peptide is at least as great as the threshold value, predicted properties for the unlabeled peptide are determined and stored on an inclusion list.

Abstract: A method for analyzing a sample can include obtaining an exclusion list of retention time and mass-to-charge ranges corresponding to high abundance compounds within a sample; separating components of the sample using the chromatographic column; obtaining a first mass data set using the mass analyzer while excluding ions within retention time and mass-to-charge ranges of the exclusion list; generating an inclusion list of features of the first mass data set; fragmenting ions corresponding to features of the inclusion list; obtaining a second mass data set from the fragmented ions; and identifying and/or quantifying low abundance compounds based on the second mass data set.

Abstract: A method of generating an inclusion list for targeted mass spectrometric analysis is disclosed. Experimentally-acquired data for a plurality of isobarically-labeled peptides derived by proteolytic digestion of a corresponding protein. The data includes, for each of the isobarically-labeled peptides, a mass-to-charge (m/z) ratio, a charge state, and a chromatographic retention time (RT). The method includes determining a hydrophobicity index (HI) of an unlabeled peptide corresponding to the isobarically-labeled peptide. If the determined HI is less than a threshold value, a substitute unlabeled peptide is selected in accordance with predetermined criteria and predicted properties for the substitute peptide are determined and stored on an inclusion list. If the determined HI for the unlabeled peptide is at least as great as the threshold value, predicted properties for the unlabeled peptide are determined and stored on an inclusion list.

Abstract: A method for analyzing a sample can include obtaining an exclusion list of retention time and mass-to-charge ranges corresponding to high abundance compounds within a sample; separating components of the sample using the chromatographic column; obtaining a first mass data set using the mass analyzer while excluding ions within retention time and mass-to-charge ranges of the exclusion list; generating an inclusion list of features of the first mass data set; fragmenting ions corresponding to features of the inclusion list; obtaining a second mass data set from the fragmented ions; and identifying and/or quantifying low abundance compounds based on the second mass data set.

Abstract: A method of generating an inclusion list for targeted mass spectrometric analysis is disclosed. Experimentally-acquired data for a plurality of isobarically-labeled peptides of interest is received at a computer. The data includes, for each of the isobarically-labeled peptides, a mass-to-charge (m/z) ratio, a charge state, and a chromatographic retention time. Predicted properties for a corresponding unlabeled peptide are determined via the computer. The predicted properties include a predicted m/z, a predicted charge state, and a predicted chromatographic retention time. The predicted properties for each corresponding unlabeled peptide are stored to the inclusion list. 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.

Abstract: A system providing environmentally friendly pathway tunnel utilizes a bottom configuration with multiple elongated beams and slots. One or more of the beams includes upstanding sedimentation members that are spaced apart along a span of the tunnel. The system interacts with the flowing water and earthen material in the flowing water such that capture and settling of the earthen material at locations along the tunnel occurs to produce a more natural water flow pathway along the tunnel.

Abstract: A system providing environmentally friendly pathway tunnel utilizes a bottom configuration with multiple elongated beams and slots. One or more of the beams includes upstanding sedimentation members that are spaced apart along a span of the tunnel. The system interacts with the flowing water and earthen material in the flowing water such that capture and settling of the earthen material at locations along the tunnel occurs to produce a more natural water flow pathway along the tunnel.

Abstract: A system providing environmentally friendly pathway tunnel utilizes bridge units having a bottom configuration with multiple elongated beams and slots. One or more of the beams includes upstanding sedimentation members that are spaced apart along a span of the tunnel. The system interacts with the flowing water and earthen material in the flowing water such that capture and settling of the earthen material at locations along the tunnel occurs to produce a more natural water flow pathway along the tunnel.

Abstract: A method of providing an environmentally appealing region for water flow along an surrounded pathway tunnel involves providing a plurality of four-sided concrete bridge units in abutting relationship to create a surrounded pathway tunnel, one end of the tunnel located upstream along a water path and an opposite end of the tunnel located downstream along the water path; allowing water to flow through the surrounded pathway tunnel during a rain or other flow event; and providing a multiplicity of the four-sided bridge units with a corresponding bottom wall structure that interacts with the flowing water and earthen material in the flowing water such that capture and settling of the earthen material at locations along the tunnel occurs to produce a more natural water flow pathway along the tunnel.