This repository provides Supplementary files and R scripts regarding multi-omics data integration that are part of the manuscripts:
Proteome capacity constraints favor respiratory ATP generation Yihui Shen, Hoang V. Dinh, Edward Cruz, et al. submitted
and part of the preprint (https://doi.org/10.1101/2022.08.10.503479)
Systematic Identification of Meaningful Metabolic Enzyme Regulation in Issatchenkia orientalis
integration of fluxomics, metabolomics, and proteomics via Michaelis-Menten kinetics
see also Hackett, S. R. et al. Systems-level analysis of mechanisms regulating yeast metabolic flux. Science 354, aaf2786–aaf2786 (2016).
Explaining flux difference between yeasts (S. cerevisiae and I. orientalis) or flux change across nutrient-limited chemostat conditions
Dataset included
fluxomics (from 13C MFA), LC-MS metabolomics, quantitative proteomics
S. cerevisiae: 12 nutrient-limited chemostats + 1 batch culture
I. orientalis: 15 nutrient-limited chemostats + 1 batch culture
Explaining flux change upon T cell activation
Dataset included
fluxomics (from 13C MFA), LC-MS metabolomics, quantitative proteomics
naive and activated mouse CD8+ T cells
Coarse-grained analysis of proteome allocation in S. cerevisiae and I.orientalis
Dataset included
protein abundance of S. cerevisiae and I.orientalis
batch culture and nutrient-limited chemostats
aerobic (+O2), anaerobic (-O2), and with antimycin treatment (+antimycin)
functional assignment of the proteome
comparison to reference proteomics from literature
Coarse-grained analysis of proteome allocation in mouse cells and tissues, and proteome efficiency of ATP generation pathways of all systems described in the manuscript
Dataset included
protein abundance of naive and activated mouse CD8+ T cells
protein abundance of mouse tissues and tumors
healthy pancreas, GEMM PDAC, flank PDAC
healthy spleen, leukemic spleen
functional assignment of mouse proteome