Patent ID: 7693665

Claim:
A method of identifying the presence of a modified peptide in a mixture of peptides by a mass spectrometry instrument comprising the steps of: generating a mass spectrum of a mixture of peptides, the mass spectrum comprising a plurality of peaks over a selected range of mass-to-charge values; determining a resolution value for at least a portion of the peaks within the range of mass-to-charge values; setting a peptide resolution value based at least on the determined resolution value; selecting one or more peaks with a resolution lower than the peptide resolution value as a putative metastable ion of a modified peptide; deriving an adjusted mass difference for a chemical moiety modifying a peptide, wherein the mass of the chemical moiety is the difference between the mass of a precursor ion of a modified peptide and a corresponding metastable ion, and wherein the deriving an adjusted mass difference takes into consideration instrument geometry as: Δ ⁢ ⁢ m amd = 2 ⁢ β ⁢ ⁢ Δ ⁢ ⁢ m - β 2 ⁢ Δ ⁢ ⁢ m 2 m where Δm amd is the derived adjusted mass difference, β is a constant that depends on geometry of the instrument; Δm is the mass of the chemical moiety, and m is a mass value falling within the selected range of mass-to-charge values, adding the derived adjusted mass difference to the mass-to-charge value of the selected peak corresponding to the putative metastable ion to derive an empirical mass-to-charge value for the precursor ion of the modified peptide; and identifying that a modified peptide is present in the mixture of peptides if a peak exists in the mass spectrum at about the empirical mass-to-charge value.