(
A) Comparison of temporal profiles of cell surface Nef- (CD4 and HLA-A) and Vpu- (CD4, tetherin and SNAT1) targets obtained by whole cell or plasma membrane proteomics. Expression levels from our whole cell proteomic analysis (WCP, red) and our previous plasma membrane profiling analysis ([
Matheson et al., 2015]; PMP, blue) are shown. Relative abundance is expressed as a fraction of maximum TMT reporter ion intensity. (
B) Dynamic range of protein regulation observed by whole cell or plasma membrane proteomics. Histograms show the frequencies of log
2 (fold change compared with mock/uninfected cells) values for proteins quantitated in our whole cell proteomic analysis (WCP, red) and our previous PMP ([
Matheson et al., 2015]; blue) at 24, 48 and 72 hr. All proteins identified by >1 unique peptide in both WCP and PMP experiments are shown. (
C–
G) Temporal profiles of selected control proteins (
C–
E), actin regulatory proteins (
F) and mitotic kinases (
G). Relative abundance is expressed as a fraction of maximum TMT reporter ion intensity. (
H) Quantitation of plasma membrane proteins by whole cell or plasma membrane proteomics. The pie chart shows overlap of proteins with Gene Ontology Cellular Compartment annotations indicative of plasma membrane localisation quantitated in our whole cell proteomic analysis (WCP, red) and our previous PMP analysis ([
Matheson et al., 2015]; blue). Protein numbers are indicated. The bar chart details the glycosylation status of proteins quantitated in WCP (red), PMP (blue) or both (tan) experiments. Glycosylation sites were identified from the UniProt Knowledgebase (accessed on 4/12/15 at
http://www.uniprot.org). Protein numbers (glycosylated/total) are indicated.