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, experiment level, and run level (SDRF), modification mass shifts for the search settings, and proteome sizes. Suppl_Table_2_Modification_Sites.tsv: List of modification sites. 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. ecoli-peptideatlas-main.zip: Code freeze of the scripts used to create the manuscript figures, downloaded 18/12/2025 Ecoli_PeptideAtlas_Supplementary.docx: Supplementary Figures of manuscript Additional files:PSMs.tsv: All PSMs integrated in the PeptideAtlas build.