1.The PTV1_sample_info.xlsx file consists of two sheets.

1. a)The first sheet the signatures of each sample treated with a single drug, where each cell line is treated with each drug for a specified duration. In this table, “sample_ID” serve as the unique identifier for each sample. The "cell_line" indicates the name of the corresponding cell line. The "pert_id" represents the ID assigned to each drug, while the "pert_name" provides the name of each drug. The "pert_time" denotes the duration of drug treatment. The "BioRep" indicates the number of biological replicates for each sample. Lastly, the "NY" represents the categorization of the cell line response to the drug as either effective or ineffective.
2. The second sheet presents the signatures of samples treated with drug combinations, where each cell line is treated with each combination of drugs at designated concentrations for a specific period. In this table, the columns "sample_ID", "cell_line", "pert_time", "BioRep", and "NY" have the same meaning as in the first sheet. Additionally, the columns "anchor" and "library" represent the two types of drugs involved in each drug combination. The design of the drug combinations can refer to: Nature, 2022, 603:166

2.PTV1_protein_matrix.csv provides the intensity values of each protein across different samples.