Annotations for each scripts

Raw data processing and filtering

• cp_frag_process.py: compile targets list from CIMAGE output, ensuring quantified peptides and standard deviation filters

• merge_comp_info_3.py: combine compiled datesets for replicates

• filter_probe_vs_probe.R: ensure every entry is a target for at least one of the two probes

• filter_20uM_competition.R: ensure every entry is enriched by corresponding probe with SILAC ratio greater than 5

• filter_200uM_competition.R: ensure every entry is enriched by corresponding probe with SILAC ratio greater than 5

• filter_competed.R: ensure every entry is competed (SILAC ratio greater than 3) by at least one of tested competitors

• filter_miscleavaged_peptide.R: remove miscleavaged tryptic peptide in isoTOP-ABPP

• filter_PDB.R: filter PDB files for structural analysis

Meta-analysis and cross-referencing

• mapping_drugbank.R: map probe targets in Drugbank database

• mapping_iBAQ.R: map probe targets in iBAQ database

• reverse_mapping_iBAQ.R: map protein entries in iBAQ dataset to probe targets dataset

• gather_families_r2.py: gather protein families information from UniProtKB database

• mapping_protein_family_separate.R: assign protein families to target list

• get_transmembrane.R: extract soluble/membrane information from UniProtKB databse and assign to targets

• get_functionalSite.py: extract functional site information from UniProtKB database

• functionalSite_analysis.R: analyze spatial distance between functional sites fetched from UniProtKB and probe labeled peptides

• fpocket_analysis.R: analyze fpocket results to obtain the overlap between fpocket predicted binding sites and probe labeled peptides

External databases for cross-reference

• drugbank_all_target_polypeptide_ids.fasta: drug target identifiers (All group, version 4.2), from Drugbank

• drugbank_nutraceutical_target_polypeptide_ids.fasta: drug target identifiers (Nutraceutical group, version 4.2), from Drugbank

• iBAQ.csv: iBAQ values in HEK293t cell line, from Supplemental Data of Geiger, T., Wehner, A., Schaab, C., Cox, J., and Mann, M. (2012). Mol Cell Proteomics 11, M111.014050.

• uniprot_sprot_human.dat: UniProtKB/Swiss-Prot Protein Knowledge database (release-2016_06), from UniProt