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Fig. 2 | Molecular Neurodegeneration

Fig. 2

From: Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimer’s disease-related proteins

Fig. 2

A high-level summary, gene ontology and pathway analysis of 4133 microglial proteins identified by TMT. a Histogram representing the distribution of microglial proteins sorted by protein wet weight (bins with proteins contributing the most wet weight are on the left). Individual protein wet weight contributions were estimated using the Perseus Proteomic Ruler analysis plugin [66], which uses measurements of histone abundance to normalize reporter abundances assuming a total wet weight density of 200 mg/ml. The cumulative distribution of protein abundance was highly dependent on a minority of proteins (of 4133 total) such that a majority of cumulative protein mass was accounted for by a small number of proteins, i.e., 5.1% of all proteins accounted for 50% of cumulative protein mass. b Comparison of relative abundance (abundance percentile rank) of proteins identified in our dataset with a reference mouse microglial proteome [8]. Abundance values of proteins identified in WT mouse microglia were binned into quartiles and compared with the reference proteome. The proportions (%) of microglial proteins are shown in each box. c Scatter plot representation of the most abundant proteins identified in our microglial proteome and the reference microglial proteome. Proteins that were among the top 10th percentile of abundance in both datasets are highlighted in red. d Results from Gene Ontology (GO) enrichment analysis of 4133 identified microglial proteins against a background list of all known mouse gene symbols (or 11,937 proteins in a total brain reference proteome) [8]. The top 10 GO terms from each of the three GO groups (Green: biological process, Purple: molecular function, Brown: cellular component) are shown. Degree of enrichment of each GO term is indicated by the Z-score (X-axis). Nearly identical results were obtained either background list of all mouse gene symbols or 11,937 mouse proteins identified in a total brain reference proteome. e Top 10 enriched functional pathways (WikiPathways) identified by enrichment analysis of 4133 microglial proteins

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