Method for determining small molecule components of a complex mixture, and associated apparatus and computer program product

An apparatus for analyzing data for one or more samples, the data for each sample being obtained from a component separation and tandem mass spectrometer system comprising a separation portion, including a liquid chromatograph, a gas chromatograph, a supercritical fluid chromatograph, or a capillary electrophoresis analyzer, and a first mass spectrometry step or provision (MS1) and a second mass spectrometry step or provision (MS2), the apparatus comprising a processor and a memory storing executable instructions that, in response to execution by the processor, cause the apparatus to at least:

• analyze, for each sample, a data set for a plurality of MS2 sample components to determine a precursor ion mass-to-charge ratio (m/z) and a retention index (RI) for each MS2 sample component;
• compare the precursor ion m/z and the RI for each MS2 sample component to precursor ion mass-to-charge ratios and retention indices of known compounds and remove any MS2 sample component from the data set corresponding to one of the known compounds, with remaining MS2 sample components in the data set being candidate MS2 sample components;
• form component clusters across the candidate MS2 sample components, each component cluster including candidate MS2 sample components each having the precursor ion m/z and the RI within respective ranges for the component cluster;
• for each sample within each component cluster, retrieve one or more MS1 sample components within the respective precursor ion m/z and RI ranges for the component cluster;
• for each component cluster, determine at most one consensus MS1 sample component, by aggregating the one or more MS1 sample components within the respective precursor ion m/z and RI ranges, to represent each sample, and associate the consensus MS1 sample component with a corresponding consensus MS2 sample component, consensus precursor ion m/z, and consensus RI determined by aggregating the MS2 sample components and associated precursor ion m/z and the RI within the component cluster;
• for each component cluster, determine whether the consensus MS1 sample component indicates a molecular ion or a derivative relationship to the molecular ion;
• group component clusters according to consensus RI and select one or more component clusters from each group of component clusters, the one or more component clusters being candidate component clusters;
• and
• correlate the consensus precursor ion m/z, the consensus RI, the consensus MS1 sample component, and the consensus MS2 sample component of the candidate component clusters with an unknown compound in the samples.

A computer program product for analyzing data for one or more samples, the data for each sample being obtained from a component separation and tandem mass spectrometer system comprising a separation portion, including a liquid chromatograph, a gas chromatograph, a supercritical fluid chromatograph, or a capillary electrophoresis analyzer, and a first mass spectrometry step (MS1) and a second mass spectrometry step (MS2), the computer program product comprising at least one non-transitory computer readable storage medium having computer-readable program code stored thereon, the computer-readable program code comprising program code for performing at least the method steps of:

• analyzing, for each sample, a data set for a plurality of MS2 sample components to determine a precursor ion mass-to-charge ratio (m/z) and a retention index (RI) for each MS2 sample component;
• comparing the precursor ion m/z and the RI for each MS2 sample component to precursor ion mass-to-charge ratios and retention indices of known compounds and removing any MS2 sample component from the data set corresponding to one of the known compounds, with remaining MS2 sample components in the data set being candidate MS2 sample components;
• forming component clusters across the candidate MS2 sample components, each component cluster including candidate MS2 sample components each having the precursor ion m/z and the RI within respective ranges for the component cluster;
• for each sample within each component cluster, retrieving one or more MS1 sample components within the respective precursor ion m/z and RI ranges for the component cluster;
• for each component cluster, determining at most one consensus MS1 sample component, by aggregating the one or more MS1 sample components within the respective precursor ion m/z and RI ranges, to represent each sample, and associating the consensus MS1 sample component with a corresponding consensus MS2 sample component, consensus precursor ion m/z, and consensus RI determined by aggregating the MS2 sample components and associated precursor ion m/z and the RI within the component cluster;
• for each component cluster, determining whether the consensus MS1 sample component indicates a molecular ion or a derivative relationship to the molecular ion;
• grouping component clusters according to consensus RI and selecting one or more component clusters from each group of component clusters, the one or more component clusters being candidate component clusters;
• and
• correlating the consensus precursor ion m/z, the consensus RI, the consensus MS1 sample component, and the consensus MS2 sample component of the candidate component clusters with an unknown compound in the samples.