Systems, methods, and computer-readable media for determining composition of chemical constituents in a complex mixture are disclosed. According to one aspect, a method for determining composition of chemical constituents in a complex mixture includes generating, using a separation tool and a mass spectrometer, separation and mass spectrometry data of a sample, wherein the separation data includes peak information and wherein the mass spectrometry data includes primary and secondary mass spectrometry data. The analysis results, including the generated separation and mass spectrometry data, are collected and stored. A chemical constituent of the sample is determined by comparing the analysis results to a library of information indicating characteristics of chemical entities, where the comparison is based on the separation and mass spectrometry information. The library of information includes data generated by the separation tool and mass spectrometer, and also includes separation and mass spectrometry data for both identified and unidentified chemical entities. An indication of the chemical constituent of the sample is made available in human-accessible form.