Mass Spectrometer Watch Mode Quantitation

The patent segments the internal standard verification process into multiple distinct mass transitions (precursor ion to fragment ion pairs) rather than relying on a single transition. By monitoring multiple segmented transitions simultaneously, the system can distinguish true internal standards from near isobaric interferences, as genuine internal standards will produce all expected fragment ions with characteristic intensity ratios, while interferences will fail to produce the complete pattern.

The patent introduces a verification mechanism that acts as an intermediary between detecting internal standard ions and triggering quantitation mode. This intermediary step checks whether multiple fragment ion transitions are present and whether their intensity ratios match expected values before allowing the quantitation trigger to activate, thereby filtering out false positives from near isobaric interferences.

The patent merges the calibration curve generation process with the target analyte quantitation analysis into a single integrated experiment. By spiking the sample with internal standards at multiple known concentrations and simultaneously acquiring data for both calibration and quantitation, the method eliminates the need for separate calibration experiments, reducing total analysis time while maintaining absolute quantitation accuracy through the use of multiple internal standard variants.

The patent makes the internal standard variants serve multiple functions: they act as both calibration standards (providing known concentration references for building the calibration curve) and as triggers for quantitation mode (initiating targeted acquisition of the target analyte). This multi-functionality allows a single experimental run to accomplish both calibration and quantitation tasks that traditionally required separate experiments.