Although several different LC-MS analysis protocols could be used (acidic, neutral, or basic sample preparation; eluent or flow variation, etc.), we selected the most frequently used (see the details in the Methods section). The duration of each experiment was 120 s (2 min). Every day, the control spectra were recorded for diethyl phthalate as a reference compound to track the state and resolution quality of each instrument. In order to enhance the RT prediction performance and standardize the spectra data from all instruments, the reference RT value identified from the control spectrum was used as the experiment condition parameter (ECP). The combined LC-MS spectrum dataset ("EnamineRT") contained 582,046 data points and includes compound SMILES, RT, and ECP values.