Proteomics: Quality Control (QC), Orthology, Enrichments, and Viral Proteins, Related to Figure 1
(A) Principal component analysis computed on intensities summarized by MSstats at the level of phosphorylation site groups within (from left to right) all runs, with one outlier run removed, and with two outlier runs removed. Outlier runs are labeled 00Hr.2 and 02.Hr.2. (B) Principal components analysis computed on protein intensities as summarized by MSstats (from left to right) within all runs, with one outlier run removed, and with two outlier runs removed. Outlier runs are both labeled 00Hr.2; one is mock and the other is infected. (C) Coefficient of variance boxplot for each condition. Black lines depict the median and their values are indicated above each boxplot. (D) Mapping detected and quantifiable proteins and phosphorylation sites from the green monkey (Chlorocebus sabaeus) protein sequences to human genes. Proteins and sites were considered quantifiable if MSstats computed a non-infinite fold change for any time point or if an infinite log2 fold change passes criteria for inclusion in any time point. (E) Intensities of viral proteins as summarized over all peptide ion fragments by MSstats, averaged across replicates. The MSstats summarization is based on the median intensity of all fragments after data pre-processing (STAR Methods). (F) Gene Ontology enrichment analysis for proteins significantly regulated in terms of abundance upon infection, separated by time point and direction of phosphorylation regulation. All terms with significant over-representation (adjusted p value < 0.01) in the regulated gene set are kept, and redundant terms are removed (see STAR Methods). Numbers in cells indicate the number of genes that match the term for a given time point and direction. (G) Gene Ontology enrichment analysis for significantly phosphorylated proteins upon infection, separated by time point and direction of protein regulation. Details same as for (F).