Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

► Good correlation between iBAQ, APEX and emPAI methods was demonstrated. ► Sum of individual protein abundances corresponded to protein concentration in cell. ► Spectral counting methods had high variation among ribosomal protein abundances. ► Higher ATP cost for biosynthetic vs. energy generation proteins ► Calculated catalytic activities were higher for energy metabolism proteins.