A system for acquiring an unknown product ion spectrum and marking isotopic product ion peaks from the unknown product ion spectrum for removal before comparing the unknown product ion spectrum with a library product ion spectrum, the system comprising: an ion source that is configured to ionize one or more compounds of a sample, producing an ion beam of precursor ions; a tandem mass spectrometer that is configured to receive the ion beam from the ion source, to select one or more precursor ions from the ion beam using a precursor ion mass selection window, to fragment precursor ions within the precursor ion mass selection window, and to mass analyze the resulting product ions, producing an unknown product ion mass spectrum for the precursor ion mass selection window; and a processor, in communication with the tandem mass spectrometer, that is configured to: receive the unknown product ion mass spectrum from the tandem mass spectrometer, retrieve from a memory a library product ion mass spectrum for a known compound, characterized in that the processor is further configured to: for each peak of the unknown product ion mass spectrum, determine if a following peak of the each peak is a potential non-halogen isotopic peak and if the following peak is a potential non-halogen isotopic peak, determine if the library product ion mass spectrum includes a peak at the same m/z value of the following peak within a threshold tolerance range, and if the library product ion mass spectrum does not include a peak at the same m/z value of the following peak within the threshold tolerance range, mark the following peak for removal from said unknown product ion mass spectrum. an ion source that is configured to ionize one or more compounds of a sample, producing an ion beam of precursor ions; a tandem mass spectrometer that is configured to receive the ion beam from the ion source, to select one or more precursor ions from the ion beam using a precursor ion mass selection window, to fragment precursor ions within the precursor ion mass selection window, and to mass analyze the resulting product ions, producing an unknown product ion mass spectrum for the precursor ion mass selection window; and a processor, in communication with the tandem mass spectrometer, that is configured to: receive the unknown product ion mass spectrum from the tandem mass spectrometer, retrieve from a memory a library product ion mass spectrum for a known compound, characterized in that the processor is further configured to: for each peak of the unknown product ion mass spectrum, determine if a following peak of the each peak is a potential non-halogen isotopic peak and if the following peak is a potential non-halogen isotopic peak, determine if the library product ion mass spectrum includes a peak at the same m/z value of the following peak within a threshold tolerance range, and if the library product ion mass spectrum does not include a peak at the same m/z value of the following peak within the threshold tolerance range, mark the following peak for removal from said unknown product ion mass spectrum. receive the unknown product ion mass spectrum from the tandem mass spectrometer, retrieve from a memory a library product ion mass spectrum for a known compound, characterized in that the processor is further configured to: for each peak of the unknown product ion mass spectrum, determine if a following peak of the each peak is a potential non-halogen isotopic peak and if the following peak is a potential non-halogen isotopic peak, determine if the library product ion mass spectrum includes a peak at the same m/z value of the following peak within a threshold tolerance range, and if the library product ion mass spectrum does not include a peak at the same m/z value of the following peak within the threshold tolerance range, mark the following peak for removal from said unknown product ion mass spectrum. for each peak of the unknown product ion mass spectrum, determine if a following peak of the each peak is a potential non-halogen isotopic peak and if the following peak is a potential non-halogen isotopic peak, determine if the library product ion mass spectrum includes a peak at the same m/z value of the following peak within a threshold tolerance range, and if the library product ion mass spectrum does not include a peak at the same m/z value of the following peak within the threshold tolerance range, mark the following peak for removal from said unknown product ion mass spectrum.