Abstract: A method of preparing a species-specific phosphorylation site peptide array for a target organism comprising: a) selecting a plurality of known non-target organism (NTO) phosphorylation site sequences and cognate known NTO phosphorylation polypeptide sequences from one or more NTO, each of the known NTO phosphorylation site sequences comprising at least 5 residues and less than 30 residues; b) identifying a matching target organism (TO) phosphorylation site sequence and cognate TO phosphorylation polypeptide sequence for one or more of the known NTO phosphorylation site sequences; c) determining the matching TO phosphorylation site sequences that correspond to orthologue polypeptides of the cognate known NTO phosphorylation polypeptide sequences; d) selecting the matching TO phosphorylation site sequences determined to correspond to orthologue polypeptides for inclusion on the array; wherein the matching TO phosphorylation site sequences that correspond to orthologue polypeptides are determined by calculating

Abstract: Method for analyzing phosphorylation data of a plurality of peptides are provided, the method comprising obtaining one or more datasets, each dataset comprising a phosphorylation signal intensity for each replicate of the plurality of peptides for a sample; transforming the phosphorylation signal intensity of each replicate of the plurality of peptides using a variance stabilizing transformation to provide a variance stabilized signal intensity for each replicate of the plurality of peptides; and identifying one or more peptides of the plurality of peptides that is/are consistently phosphorylated or consistently unphosphorylated.