Extended Data Fig. 1: Biological replicates show good reproducibility, with differences revealing biological phenomena.
a, Rarefaction analysis of the proteome coverage (proteins with at least two unique peptides in each mass spectrometry run) as a function of the number of mass spectrometry runs. b, Distribution of log2-transformed fold change differences between the two biological replicates. c, Scatter plot of protein fold changes between all biological replicate measurements (n = 1,512,475; all proteins, all temperatures, all mutants). r depicts Pearson correlation. d, Reproducibility of protein fold changes between biological replicate measurements at each temperature. e, Examples of replicate correlation for specific mutants, highlighting that flagellar proteins are common outliers in one of the two clones (nΔhemX = 13,150, nΔybaB = 12,313, nΔclpA = 12,950, nΔmrcB = 12,604, nΔfur = 12,543, nΔmlaA = 12,559, nΔlpp = 12,719; all proteins, all temperatures). f, Polymerase chain reaction of the promoter region of the flhDC operon (schematic on top) demonstrates the presence of insertions in mutant clones (gel on bottom, n = 1; for gel source data see Supplementary Fig. 2) with high flagellar protein expression (FliC fold-changes at the two lowest temperatures of each mutant replicate used as a proxy for abundance). g, Scatter plot of abundance and thermal stability z-scores of all proteins in all mutants (n = 170,150). r depicts Pearson correlation. h, Distribution of the number of mutants in which a protein is significantly altered (n = 1,764 proteins). Box plots as in Fig. 2a. i, Distribution of the number of proteins that are significantly altered in each mutant (n = 121 mutants). Box plots as in Fig. 2a.
