Table S2. Anchor protein absolute quantification

To investigate the correlation between peptide concentration and SWATH signal intensity and to determine the lower limit of quantification for every stable isotope labelled standard peptide, a dilution series experiment spanning 30 to 0.1 fmol/μg in a constant background (1 μg Mtb whole cell lysate) was performed (sheet “Dilution series”). All peptides showed a good linear correlation as indicated by a Pearson R2 above 0.94, slopes close to 1 and axis intercepts close to 0. Furthermore, quantified endogenous peptide concentrations were not significantly lower than the lower limit of quantification determined by the dilution series experiment. Absolute peptide abundances for 51 peptides representing 30 anchor proteins are given in sheet “Absolute peptides”. Absolute protein abundances for 30 anchor proteins are given in sheet “Absolute proteins”. For those proteins for which two absolutely quantified peptides were available, individual peptide concentrations were averaged. Concentrations are given in fmol peptide per μg of total cell extract (fmol/μg). Abbreviation: CAM = Carbamidomethylation