Patent ID: 7897405

Claim:
A method for determining a time of elution of a peptide of interest from a liquid chromatography column, comprising: providing a sample containing the peptide of interest; loading at least a portion of the sample onto the liquid chromatography column; subjecting a portion of an eluate from the liquid chromatography column containing the peptide of interest to selective reaction monitoring, comprising obtaining a chromatogram along a common chromatographic time scale for each one of a plurality of candidate fragment ions of the peptide of interest; determining a quality of overlay between the candidate fragment ions along the common chromatographic time scale by computing an OverlayScore relating to an expected correlation between each of the plurality of candidate fragment ions of the peptide of interest in chromatographic time; and, assigning a time along the common chromatographic time scale as the time of elution of the peptide of interest based on the determined quality of overlay between the candidate fragment ions; wherein the OverlayScore at time s for a parent ion of m/z value M is computed according to the equation OverlayScore ⁡ ( s , M ) = ∑ i = 0 N ⁢ Overlay ⁡ ( s , M / m i ) N wherein Overlay(s, M/m i ) is the computed correlation between the chromatograms for the i th fragment ion of m/z value m i and the sum of all fragment ions other than the i th fragment ion.