Extended Data Fig. 2: Targeted proteomics (Dataset 2).

a, Table listing peptides used for quantifying producer, consumer and mixed populations by targeted proteomics (PRM) assays. The Fragments column lists the top3 fragments not shared by the two isobaric mixed labelling state precursors, which were used for quantification. The CE column indicates the collision energies used, as predicted by Skyline. b, Similar results are obtained with quantification of intact precursors as with the top3 suitable fragments. Shown are all individual data points from Dataset 2. The Pearson correlation between both quantification strategies is 0.993. Quantification at MS1 level can be useful when the signal is low, as was the case for FAC-sorted populations shown in Fig. 4. c, Similar results are obtained when peptides with missed cleavages from tryptic digests are used. The data shown is from an independent experiment otherwise similar to the one shown in Fig. 2. The data shown is the average of the top three fragments of three measured peptides across two biological replicates. Error bars show the standard deviation. d, Uncropped images of colonies grown in a 12-well plate (cropped version shown in Fig. 2A). Each day, the plate was scanned and a column of colonies was harvested (right to left), resulting in a pseudo timecourse. e, Targeted proteomics experiment investigating peptides with three lysine residues. Two biological replicate samples (200 μM lysine, 48 h) from the experiment shown in Fig. 2 were remeasured with a targeted method that included peptides with three lysine residues (as well as two peptides with two lysine residues, as control). MS1 data was used for quantification. The depletion of the mixed labelling states is apparent also in peptides with three lysine residues.