Protein degradation and growth dependent dilution substantially shape mammalian proteomes

This repo contains all of the relevant data files contained for running the analysis from the paper. If you want to reproduce the anaysis, the R scripts on the github will call these files. It also contains some initial processed data that might be useful like protein and clearance rate by sample matricies.

• Files needed for analysis, go analysis and mapping protein to gene names
  • GO_Human.txt
  • GO_Mouse.gmt
  • Mouse.fasta

• Processed half life and coppy number data from Schwanhäusser et al.
  • Schwanhauser_et_al.csv

• Processed half live and abuncance data from MS fragger research of of raw data from Mathieson et al.
  • Hepatocytes.csv
  • NKcells.csv
  • Bcells.csv
  • Monocytes.csv

• Downstream outputs from this analysis and half lives reported by Mathieson et al.
  • Savitski_halflives.csv

• Protein concentrations used from Riekman et al for resting and activated B-Cells.
  • Act_rest_Bcells.csv

• Mouse tissue metabolic labeling meta data
  • Miceotopes_file_annotations.csv

• Mouse tissue metabolic labeling searched data
  • report_lysc.tsv
  • report_trypsin.tsv
  • report_trypsin_ultra.tsv
  • report_recycle.tsv (Variable mod search for recycling)

Processed Data matricies:

• Ultra_trypsin_half_lives.csv
• Ultra_trypsin_Abundance.csv
• Exploris480_LysC_half_lives.csv
• Exploris480_LysC_Abundance.csv