A method for non-targeted determination of composition of chemical constituents in a complex mixture, the method comprising: generating, using chromatography and a mass spectrometer separation and mass spectrometry data of a sample, wherein the separation data includes peak information and retention index information, wherein the peak information specifies a chromatographic peak associated with a particular mass-to-charge ratio representing the presence or absence of one or more ions across an axis representing separation, and wherein the mass spectrometry data includes primary and secondary mass spectrometry data; collecting and storing analysis results, the analysis results including the generated separation and mass spectrometry data; determining a chemical constituent of the sample by comparison of the analysis results to a library of information indicating characteristics of chemical entities, wherein the comparison is based on the separation and mass spectrometry data, wherein the library of information comprises data generated by chromatography and mass spectrometer, wherein the library of information contains data that was generated by chromatography and the mass spectrometer using a reference standard, and wherein the library of information includes separation and mass spectrometry data for identified and unidentified chemical entities; determining a degree of confidence for the determination of the chemical constituent of the sample; and displaying, in a graphical user interface, an indication of the chemical constituent of the sample, the degree of confidence for the determination of the chemical constituent of the sample, and library information for a particular entity in the library along with at least some of the analysis results so that a user may perform a visual comparison of the two or visually confirm the correctness of the comparison. generating, using chromatography and a mass spectrometer separation and mass spectrometry data of a sample, wherein the separation data includes peak information and retention index information, wherein the peak information specifies a chromatographic peak associated with a particular mass-to-charge ratio representing the presence or absence of one or more ions across an axis representing separation, and wherein the mass spectrometry data includes primary and secondary mass spectrometry data; collecting and storing analysis results, the analysis results including the generated separation and mass spectrometry data; determining a chemical constituent of the sample by comparison of the analysis results to a library of information indicating characteristics of chemical entities, wherein the comparison is based on the separation and mass spectrometry data, wherein the library of information comprises data generated by chromatography and mass spectrometer, wherein the library of information contains data that was generated by chromatography and the mass spectrometer using a reference standard, and wherein the library of information includes separation and mass spectrometry data for identified and unidentified chemical entities; determining a degree of confidence for the determination of the chemical constituent of the sample; and displaying, in a graphical user interface, an indication of the chemical constituent of the sample, the degree of confidence for the determination of the chemical constituent of the sample, and library information for a particular entity in the library along with at least some of the analysis results so that a user may perform a visual comparison of the two or visually confirm the correctness of the comparison.