Level_1_data_methods	"The data at this level is the raw MS2 counts of identified proteins for cultured cell samples treated with various drugs. The raw MS data is processed by the *MaxQuant* software (version 1.6.0.13) which uses its *Andromeda* search engine to detect intensity peaks, search and score matched peptides, map to related protein groups, and quantify protein abundance by various measures."
Level_1_data_QC_methods	
Level_2_data_methods	The data at this level is the first-level normalized MS2 counts of identified proteins transformed by the counts of corresponding HeLa cells measured in the same SDS-PAGE gel during the MS assay process. The raw MS2 counts of identified proteins of each cultured cell sample are divided by a normalization coefficient calculated as the MS2-counts ratio between the HeLa cell measured in the same SDS-PAGE gel and a reference HeLa cell.
Level_2_data_QC_methods	
Level_3_data_methods	"The data at this level is the second-level normalized MS2 counts of identified proteins performed for all cell samples within each cell culture experiment. The MS2 counts of identified proteins of all cultured cell sample within each cell culture experiment are normalized by standard CPM/RPKM normalization method, after outlier cell samples are removed by the correlation-based clustering analysis."
Level_3_data_QC_methods	
Level_4_data_methods	"The data at this level is the differentially expressed proteins within each cell culture experiment at drug treatment for each cell line. The differentially expressed proteins are generated by the *edgeR* program which compares the expression levels of two groups of sample replicates, the drug-treated group and the control group within each cell culture experiment at drug treatment for each cell line, by testing the statistical significance of the difference in their expression levels."
Level_4_data_QC_methods	
Level_5_data_methods	"Top-ranked differentially expressed proteins were subjected to standard and dynamic enrichment analysis using Gene ontology and the Molecular Biology of the Cell Ontoloy. Standard enrichment analysis uses Fisher's exact test to analyze, if a list of proteins significantly overlaps with a list of proteins that are annotated to a single SCP, dynamic enrichment analysis analyzes, if a list of proteins significantly overlaps with a lost of proteins that are annotated to a network of functionally interacting SCPs."
Level_5_data_QC_methods	
