Statistical analysis of MERS-CoV-infected cells.

For analyses of proteomics, lipidomics, and metabolomics data from the Calu-3 cells infected with MERS-CoV, the quantitative data profiles were evaluated for extreme outlier behavior (47). No outlier samples were observed in the metabolomics and lipidomics data; however, one proteomics replicate from the infected group showed extremely poor coverage and correlation, indicating an issue with the protein extraction. That one sample was removed from subsequent analyses. Further quality assessment of the proteomics data included evaluation of individual peptides to identify those with inadequate coverage for either statistical analyses or protein quantification (46). Metabolomic and lipidomic data were normalized via standard median centering, and proteomics data were normalized via median centering against a rank-invariant peptide subset identified to reduce bias (48). To allow evaluation of the proteomic data at the protein level, a signature-based protein quantitation methodology was employed (49). Finally, the protein, metabolite, and lipid data were evaluated for quantitative differences between the results of mock infection and MERS-CoV infection via a standard two-sample t test.