A key process in signal transduction is the addition of phosphate groups to proteins, i.e. phosphorylation mediated by protein kinases. Determining kinase-substrate specificity given a set of phosphorylated peptides is therefore of significance for understanding signal transduction. One arm of protein kinase action is sequence specificity, which can be considered a pattern recognition problem at sites of phosphorylation. Here, the position probability matrix method is implemented to build models of kinases given targeted peptides, visualise resultant models as motifs and test significance of models against phospho-proteomic input data. The utility of a number of functions implemented in R is demonstrated by application to phospho-proteomic data.