Hardware components and software modules were configured to enhance the automation, efficiency, and reliability of a commercial open access atmospheric pressure ionization mass spectrometry (API/MS) system for flow injection analysis. The data massaging module is a versatile package for data manipulation/reduction which is initialized upon detecting the end of data acquisition and can function in parallel during the data acquisition of the next sample. The data interpretation module compares the ions in the acquired mass spectrum with the predicted molecular adduct ions in different charge states, as well as the predicted isotopic distributions, possible artifact, polymer/cluster, byproduct/fragmentation ions, and then uses the results to score the quality of the spectrum. The e-mailing module transmits the spectrum and interpretation report to the desktop computer of the submitting chemist where the spectrum can be displayed and the report viewed. A scheme is also presented for the automated interpretation of an API mass spectrum for the determination of the most likely molecular weights of the components present in an “unknown” sample. Related flow diagrams, algorithms, and applications are illustrated.