Result files associated with the publication: "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al. The following files are included in the archive: Raw max-marginal predictions using LC-MS²Struct for all LC-MS² experiments of the ALLDATA setup Averaged max-marginals for the LC-MS²Struct over all SSVM models Top-k accuracies for the comparison methods (MS²+RT, ...) Ranks for the ground-truth structures predicted by Only MS² and LC-MS²Struct (molecule class analysis) Instructions: clone the repository containing the experimental scripts and analysis notebooks: https://github.com/aalto-ics-kepaco/lcms2struct_exp download the archive in this repository unpack the archive in the git-repository root directory follow the instructions given in the README.md of the git-repository to reproduce the figures, etc. Version history: Version 1: Experimental results for "Method comparison" and "Molecule classification analysis" where performed with 2D fingerprints (preprint v1) Version 2 (this version): Experimental results for "Method comparison" and "Molecule classification analysis" where performed with 3D fingerprints