Use of windowed mass spectrometry data for retention time determination or confirmation

A method for scoring peaks of a known compound of interest from a collection of mass spectra, comprising:

• obtaining a collection of mass spectra for a plurality of time intervals, wherein one or more compounds are separated from a sample mixture using a separation device and wherein one or more mass spectrometry scans are performed on the separating sample mixture at each time interval of the plurality of time intervals using one or more sequential mass window widths in order to span the entire mass range producing a collection of mass spectra for the plurality of time intervals using a mass spectrometer;
• selecting a fragment ion of a known compound;
• calculating an extracted ion chromatogram (XIC) for the fragment ion from the collection of mass spectra, wherein the XIC includes an intensity of the fragment ion for each time interval of the plurality of time intervals;
• and
• if two or more XIC peaks corresponding to the fragment ion are found in the XIC two or more different time intervals, scores each XIC peak in order to determine an actual retention time for the known compound by obtaining a mass spectrum of the entire mass range from the collection of mass spectra for each of the two or more different time intervals, and comparing values of one or more ion characteristics of a mass-to-charge ratio (m/z) peak of the fragment ion in each entire mass range mass spectrum to one or more known values for the fragment ion.

A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for scoring peaks of a known compound of interest from a collection of spectra, the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a measurement module and an analysis module;
• obtaining a collection of mass spectra for a plurality of time intervals using the measurement module, wherein one or more compounds are separated from a sample mixture using a separation device and wherein one or more mass spectrometry scans are performed on the separating sample mixture at each time interval of the plurality of time intervals using one or more sequential mass window widths in order to span the entire mass range producing a collection of mass spectra for the plurality of time intervals using a mass spectrometer;
• selecting a fragment ion of a known compound using the analysis module;
• calculating an extracted ion chromatogram (XIC) for the fragment ion from the collection of mass spectra, wherein the XIC includes an intensity of the fragment ion for each time interval of the plurality of time intervals using the analysis module;
• and
• if two or more XIC peaks corresponding to the fragment ion are found in the XIC at two or more different time intervals, scores each XIC peak in order to determine an actual retention time for the known compound by obtaining a mass spectrum of the entire mass range from the collection of mass spectra for each of the two or more different time intervals, and comparing values of one or more ion characteristics of a mass-to-charge ratio (m/z) peak of the fragment ion in each entire mass range mass spectrum to one or more known values for the fragment ion.