Methods and Apparatus for Identifying Ion Species Formed during Gas-Phase Reactions

An apparatus comprising:

• a chromatograph for providing a stream of at least partially separated chemical substances;
• a mass spectrometer having an atmospheric pressure ion source within an ionization chamber fluidically coupled to the chromatograph for generating one or more progenitor ion types from each chemical substance;
• a first vacuum chamber of the mass spectrometer operable to receive the progenitor ion types, the interior of which is at a pressure in a range of 750 mTorr to 50 Torr;
• a set of electrodes operable to apply an accelerating potential to the progenitor ion types within or across at least one of the ionization chamber or the first vacuum chamber so as to generate a plurality of product ion types by in-source fragmentation;
• a mass analyzer and detector of the mass spectrometer operable to receive and detect abundance data for each progenitor ion type and each product ion type;
• and
• a programmable electronic processor electrically coupled to the detector, the programmable processor comprising instructions operable to cause the programmable processor to:
• receive the abundance data for each of the progenitor ion types and product ion types detected by the detector during a time range;
• automatically detect and characterize chromatogram peaks as a function of time for each of a plurality of mass-to-charge ratio ranges of the abundance data for the progenitor ion types and product ion types;
• automatically generate synthetic analytical fit peaks to the detected chromatogram peaks;
• automatically perform a respective cross-correlation score calculation between each pair of synthetic analytical fit peaks;
• and
• automatically recognize matches between progenitor ion types and product ion types based on the cross correlation scores.