Phosphopeptide intensity data were summarized at the peptide ion level along with confident localization of phosphorylation as described in the previous section. Quantification of phosphorylation based on peptide ions were processed using artMS as a wrapper around MSstats, via functions artMS::doSiteConversion and artMS::artmsQuantification with default settings. All peptides containing the same set of phosphorylated sites were grouped and quantified together into phosphorylation site groups. For both phosphopeptide and protein abundance MSstats pipelines, MSstats performs normalization by median equalization, imputation of missing values and median smoothing to combine intensities for multiple peptide ions or fragments into a single intensity for their protein or phosphorylation site group, and statistical tests of differences in intensity between infected and control time points.