This folder contains data relating to Figure 2 and Extended View 2B+E
20210602_KgluC_labelMod_permut_2022-08-24_12-17-54.sky - Main experiment measuring labelling states of peptides containing 2 lysine residues in colonies grown on 13C glucose supplemented with 4 different lysine concentrations, over 3 timepoints, in 2 biological replicates.
20220906_KgluC_3lysine_2022-09-21_10-33-32.sky - Additional experiment shown in Extended View 2E where two samples from theabove experiment were remeasuredto look at peptides with three lysine residues.
Yeast colonies were grown for 1,2 or 3 days on minimal media with 1% 13C glucose and various amounts of unlabelled lysine. Proteome samples from whole colonies were prepared by reduction-alkylation and digestion with gluC. The labelling state of a selected number of peptides containing two lysine residues was determined in 20210602_KgluC_labelMod_permut_2022-08-24_12-17-54.sky. This experiment contains data for 4 different lysine supplementation concentrations, 3 different timepoints and 2 biological replicates (one raw data file each, file name contains all relevant information). The two samples remeasured in 20220906_KgluC_3lysine.sky are the two biological replicates harvested at 48h supplemented with 200uM lysine. We additionally provide 28 raw data files, the skyline reports used for downstream analysis and Jupyter notebooks containing the code used to generate the figures in the publication.
This folder contains data relating to Extended View 2C
20210810_K_missedCleavage_2022-08-24_15-23-40.sky - Using missed cleavage peptides from tryptic digests (instead of gluC digests) to quantify producer/consumer labelling states.
Yeast colonies were grown for up to 3 days on minimal media with 1% 13C glucose and various amounts of unlabelled lysine. Proteome samples from whole colonies were prepared by reduction-alkylation and digestion with trypsin. The labelling state of a selected number of peptides containing two lysine residues was determined (these were missed cleavage peptides). This folder contains one Skyline document and 24 raw data files, the skyline report used for downstream analysis. Note the unusual "minus0.001" modification applied to one of the mixed labelling state precursors and see the following Skyline forum support thread for more information: https://skyline.ms/announcements/home/support/thread.view?entityId=8ebed690-dbfa-1039-a3a0-e465a393713c&_docid=thread%3A8ebed690-dbfa-1039-a3a0-e465a393713c
This experiment contains data for 3 different lysine supplementation concentrations, 4 different timepoints and 2 biological replicates (one raw data file each, file name contains all relevant information).
This folder contains data relating to Extended View 1
20210923_K_missedCleavage_2022-08-24_12-59-30.sky - Investigation of lysine producer/consumer subpopulations in liquid yeast cultures using targeted 13C proteomics
Liquid batch cultures of yeast were grown in minimal media containing 1% 13C glucose and 68mM lysine. Proteome samples were prepared by reduction-alkylation and digestion with trypsin. The labelling state of a selected number of peptides containing two lysine residues (missed cleavage peptides) was determined. This folder contains one Skyline document, 18 raw data files, a metadata table in csv format, the skyline report used for downstream analysis. This experiment contains 4 biological replicates. Cultures were samples at four different timepoints, few hours apart. Samples are numbered 1-16, the corresponding metadata can be found in the csv table included with the raw data files. Note the unusual "minus0.001" modification applied to one of the mixed labelling state precursors and see the following Skyline forum support thread for more information: https://skyline.ms/announcements/home/support/thread.view?entityId=8ebed690-dbfa-1039-a3a0-e465a393713c&_docid=thread%3A8ebed690-dbfa-1039-a3a0-e465a393713c
This folder contains data relating to Extended View 3
20220826_L_2022-08-26_16-07-34.sky - Investigation of producer/consumer subpopulations in yeast colonies supplemented with leucine
20220824_F_2022-08-26_16-01-27.sky - Investigation of producer/consumer subpopulations in yeast colonies supplemented with phenylalanine
20220825_N_2022-08-26_12-34-34.sky - Investigation of producer/consumer subpopulations in yeast colonies supplemented with asparagine
Yeast colonies were grown for 1,2 or 3 days on minimal media with 1% 13C glucose and various amounts of three different amino acids (leucine, asparagine, phenylalanine). Proteome samples from whole colonies were prepared by reduction-alkylation and digestion with trypsin. The labelling state of a selected number of peptides containing two residues of the supplemented amino acid was determined. This folder contains three Skyline document, raw data files, the skyline reports used for downstream analysis and a Jupyter notebook containing the code used to generate the figures in the publication. This experiment contains data for 3 different amino acids, 3 different timepoints, 3 different concentrations, each in biological duplicates (one raw data file each, file name contains all relevant information). Note the unusual "minus0.001" modification applied to one of the mixed labelling state precursors and see the following Skyline forum support thread for more information: https://skyline.ms/announcements/home/support/thread.view?entityId=8ebed690-dbfa-1039-a3a0-e465a393713c&_docid=thread%3A8ebed690-dbfa-1039-a3a0-e465a393713c