Data Independent Acquisition of Product Ion Spectra and Reference Spectra Library Matching

A method quantitating detectable compounds of a sample, comprising:

• receiving sample product ion spectra for each mass selection window of a plurality of precursor mass selection windows for each time step of a plurality of time steps using a processor, wherein the sample product ion spectra are produced by separating detectable compounds in a sample over time, and at each time step analyzing the detectable compounds by performing a plurality of product ion scans for a plurality of precursor mass selection windows selected across a mass range of the sample using a tandem mass spectrometer;
• and
• searching the received sample product ion spectra for the presence of one or more known compounds of interest with known product ion spectra using the processor by, for each known compound:
• a) retrieving a known product ion spectrum from a library,
• b) retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectrum,
• c) generating sample product ion traces in time from the sample product ion spectra for a set of known product ions from the known product ion spectrum,
• d) calculating a correlation score for each trace of the sample product ion traces that represents how well a known product ion of the set and the each trace match and that represents how well a peak shape of the each trace correlates to peak shapes of the other traces of the sample product ion traces, and
• e) calculating a quantitative value for the known compound from the sample product ion traces that have correlation scores that exceed a threshold value.

A computer program product, comprising a tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for quantitating detectable compounds of a sample, 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
• receiving sample product ion spectra for each mass selection window of a plurality of precursor mass selection windows for each time step of a plurality of time steps using the measurement module, wherein the sample product ion spectra are produced by separating detectable compounds in a sample over time, and at each time step analyzing the detectable compounds by performing a plurality of product ion scans for a plurality of precursor mass selection windows selected across a mass range of the sample using a tandem mass spectrometer;
• and
• searching the received product ion spectra for the presence of one or more known compounds with known product ion spectra using the measurement module by, for each known compound:
• a) retrieving a known product ion spectrum from a library,
• b) retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectrum,
• c) generating sample product ion traces in time for from the sample product ion spectra for a set of known product ions from the known product ion spectrum,
• d) calculating a correlation score for each trace of the sample product ion traces that represents how well a known product ion of the set and the each trace match and that represents how well a peak shape of the each trace correlates to peak shapes of the other traces of the sample product ion traces, and
• e) calculating a quantitative value for the known compound from the sample product ion traces that have correlation scores that exceed a threshold value.