Abstract: Methods of identifying predicted or actual structures of members of a chemical or physical library are provided. The methods provide for the direct identification of compound structure following combinatorial synthesis using molecular mass measurements of individual compounds, thereby eliminating the necessity of encoding synthetic steps. The analysis of mass spectrometric data for sets of related compounds reveals compounds that are missing in a group of related compounds and identifies compounds that do not belong to a group of related compounds due to unexpected chemical, physical, or biological transformations. The methods may be applied to any group of compounds originating from chemical reactions where one reactant is common to the synthetic transformation. One particular application of these methods is in the analysis of the products of combinatorial synthesis. Systems, computer programs products, and kits are additionally provided.