Fig. 5: Effects of common extraction modalities on proteomics and metabolomics in multiple sample types.
From: A diverse proteome is present and enzymatically active in metabolite extracts
a BCA determination of protein content, normalized by starting tissue amount across AMW20, Bligh-Dyer aqueous phase (BD-aq), 80% methanol, and BD-organic phase (BD-org) in murine liver extractions (mean ± SD, n = 3 technical replicates per group). b Upset plot depicting protein intersections between the four extraction conditions (n = 3 technical replicates per group). c GSEA of BD-aq versus AMW20 Biological processes with the top 5 most impacted pathways based on FDR q-values labelled. Gene set enrichment analysis (biological processes) of proteins significantly impacted extraction type. The top 10 pathways (based on FDR q-values) are labelled, and significantly enriched pathways relative to the whole liver metabolome by GeneRatio are colored in red. d GSEA MeOH versus AMW20 gene set enrichment analysis (biological processes) of proteins significantly impacted by extraction method. Gene set enrichment analysis (biological processes) of proteins significantly impacted by extraction type. The top 10 pathways (based on FDR q-values) are labelled, and significantly enriched pathways relative to the whole liver metabolome by GeneRatio are colored in red. e Heatmap depicting relative abundance of “small molecule catabolic process”-associated proteins across extraction conditions and row standardized. All differentially abundant proteins (based FDR p-value) are shown. Significance calculated via LIMMA-eBayes (t-stat, two-sided) on Log2 transformed proteins without any missing values. f Top 5 most extraction water-content impacted biological processes based on FDR q-values within each matrix. Matrices include murine liver, adipose, brain, muscle, and plasma, and human Phoenix-AMPHO (HEK293) cells (n = 3 technical replicates per group).
