Fig. 4
From: An integrated toolkit for human microglia functional genomics
Global proteome profiling of iMG. A. Venn-diagram showing the number of proteins detected by diaPASEF and PASEF mass spectrometry (MS) in lysates from iMG (day 21). B. Dot plot showing the correlation between iMG mRNA expression (scRNA-Seq), and proteins expression measured in diaPASEF (Tb= 0.2764, p-value = 5.550e− 201; Pearson’s r = 0.3794 and p-value = 6.1881e− 182). Each dot is a gene/protein pair. C. Scatter plot shows the abundance of proteins expressed in iMG. Global protein abundance was obtained using diaPASEF proteomics. On the graph, proteins are ordered based on their expression levels. Each dot represents a protein. The protein abundances were divided into four quartiles (Q: quartile). Microglial signature proteins were detected in quartile 1 and 2. D. Bar and dot hybrid plot showing the high expression of microglia signature proteins compared to the expression of proteins considered to be monocyte specific. Proteins abundance measured in diaPASEF methods is shown in the left y-axis while the right y-axis shows proteins abundance detected in conventional PASEF method. E. Venn-diagram is showing the comparison of iMG proteome with the proteome of 5000 pMG from a previous study (Olah, M. et al. 2018). Most of the proteins expressed in pMG overlapped with the proteome of iMG. F. GO analysis of most abundant proteins identified in iMG MS. Lollipop chart (ShinyGO) provides information about Biological Processes (BP), fold enrichment significance (FDR in log10) and number of genes (size of the circle) in each BP identified. G. Pathways analysis results of proteins identified in iMG MS. The most significant 20 pathways are shown. Dot plot shows the top 20 enriched pathways, significance (FDR in log10), and the number of genes in each pathway shown. Cellular lysate from C1-iPSC line was used for MS. Abbreviations: PASEF parallel accumulation serial fragmentation; diaPASEF data independent acquisition parallel accumulation serial fragmentation; iMG induced pluripotent stem cell derived microglia; pMG primary microglia; FDR false discovery rate