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EBprot is a statistical tool for differential expression of proteins in labeling-based proteomics experiments. The tool directly models the distribution of peptide-level ratios and scores each protein based on consistent evidence across the peptides, in contrast to the common practice of assigning p-values to protein-level ratios which loses reproducibility information.

The modules presented here contain an improved extension of EBprot (version 1) offering flexible semi-parametric modeling which is more robust in handling heavily skewed or multi-modal data, like ratio data.

The principal method (version 1) was published here (Koh et al, Proteomics 2015).