Methods and systems for matching product ions to precursor in tandem mass spectrometry

Abstract

Methods of tandem mass spectrometry (MS/MS) for use in a mass spectrometer are disclosed, the methods characterized by the steps of: (a) providing a sample of precursor ions comprising a plurality of ion types, each ion type comprising a respective range of masses; (b) generating a mass spectrum of the precursor ions using the mass spectrometer so as to determine a respective mass value or mass value range for each of the precursor ion types; (c) estimating an elemental composition for each of the precursor ion types based on the mass value or mass value range determined for each respective ion type; (d) generating a sample of fragment ions comprising plurality of fragment ion types by fragmenting the plurality of precursor ion types within the mass spectrometer; (d) generating a mass spectrum of the fragment ion types so as to determine a respective mass value or mass value range for each respective fragment ion type; (e) estimating an elemental composition for each of the fragment ion types based on the mass value or mass value range determined for each respective fragment ion type; and (f) calculating a set of probability values for each precursor ion type, each probability value representing a probability that a respective fragment ion type or a respective pair of fragment ion types was derived from the precursor ion type. Some embodiments may include a step (g) of generating a synthetic MS/MS spectrum for each respective precursor ion type based on the calculated probability values.