Table 1. Main analysis customization input parameters and their default values (Full table of input options is presented in Supplementary Table S1).

Parameter	Default	Description
Clustering method	NONE	Cluster phospho-peptides using either PCA & k-means (19) or mclust (20)
Ratio Cutoff	3	Threshold for phospho-peptide intensity ratio
Correlation Method	Spearman	Choose correlation index among Spearman, Pearson and Kendall tau.
Correlation Cutoff	0.8–0.9	Correlation coefficient threshold. Default 0.9 for Pearson, 0.8 for Spearman or Kendall tau
Correlation P-value Cutoff	0.05	Threshold for significance of correlation of phospho-peptide profiles