Method of mass spectrometry

A mass spectrometer for performing data independent acquisition mass spectrometry on a sample to which an isotopologue of a target analyte is added, the mass spectrometer comprising:

• an ionisation source for producing a plurality of precursor ions;
• a mass analyser;
• a fragmentation apparatus;
• a mass selector;
• a chromatography system configured to separate molecules of the sample upstream from the mass selector;
• and
• a controller configured:
• to cause the ionisation source to ionise the sample and isotopologue as they elute from a chromatography system to form precursor ions;
• to cause the mass spectrometer to mass analyse the precursor ions using a data independent acquisition (DIA) methodology comprising performing mass analysis scans in the MS1 domain and performing mass analysis scans in the MS2 domain;
• and
• to identify that the isotopologue is eluting from the chromatography system by analysing MS1 scan data for mass spectral peaks corresponding to the isotopologue, wherein upon the controller identifying that the isotopologue is eluting the controller is further configured to cause the mass spectrometer to perform a plurality of target scans each having a target isolation window including a mass to charge ratio representative of the target analyte over a duration of a chromatographic peak of the isotopologue for at least one of identification and quantitation of the target analyte,
• wherein the target scans are configured to provide additional quantitation data for the target analyte.

A computer program product comprising one or more non-transitory computer-readable media having computer instructions stored therein, the computer program instructions being configured such that, when executed by one or more computing devices, the computer program instructions cause the one or more computing devices to:

• cause an ionisation source to ionise a sample and an isotopologue as they elute from a chromatography system to form precursor ions;
• cause a mass spectrometer to mass analyse the precursor ions using a data independent acquisition (DIA) methodology comprising performing mass analysis scans in the MS1 domain and performing mass analysis scans in the MS2 domain;
• and
• identify that the isotopologue is eluting from the chromatography system by analysing MS1 scan data for mass spectral peaks corresponding to the isotopologue, wherein upon the controller identifying that the isotopologue is eluting the computer program instructions cause the one or more computing devices to:
• cause the mass spectrometer to perform a plurality of target scans each having a target isolation window including a mass to charge ratio representative of the target analyte over a duration of a chromatographic peak of the isotopologue for at least one of identification and quantitation of the target analyte,
• wherein the target scans are configured to provide additional quantitation data for the target analyte.