This repository contains a collection of supplementary data and scripts for analyzing and visualizing the data pertaining to the study:
Proteome re-allocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media.
In this study, Saccharomyces cerevisiae strain CEN.PK113-7D was cultivated in bioreactors with glucose as carbon source with or without supplementation of amino acids, both aerobically and anaerobically.
The main script Organize_filter_and_quantify_proteomics.R is used to normalize the TMT data into mass-percentages. The result of running this script is 6 data files named glu_proteomics_*.csv that are used throughout the analysis. Input data for the script are TMT_aerobic_cultures.csv, TMT_anaerobic_cultures.csv and ref2824_iBAQ_unique_peptides.csv. For the iBAQ-file, fmol/ug amounts and Uniprot accessions were obtained from the proteomics analysis and matched to gene names obtained from Uniprot. All original proteomics data can be obtained from the PRIDE database using accession numbers PXD018361 and PXD012803.
- R studio (version 1.0.136 or later)