The E. coli PeptideAtlas Build: Characterizing the observed Escherichia coli Pan-proteome and its post-translational modifications

Suppl_Table_1_Project_and_Run_Metadata: Metadata on project level and run level (SDRF). Suppl_Table_2_exp_contrib_table.tsv: List of all included projects and how they were split up into experiments, also includes metadata and identification rate statistics. Identical to the list that is shown on the build webpage. Suppl_Table_3_Modification_Sites.tsv: Mass shifts, Unimod names, classifications, and modified residues of the modification sites uniquely mapping to a canonical protein in the build. Note that for the position in the protein, placeholder values were used for protein C- and N-terminal modifications. Suppl_Table_4_PSMs.tsv: All PSMs integrated in the PeptideAtlas build. ecoli-peptideatlas-main.zip: Code freeze of the scripts used to create the manuscript figures, downloaded 28/07/2025