EBprot

EBprotV2 is an advanced version of the EBprot software, designed as a Perseus plugin to facilitate peptide-ratio-based differential protein abundance analysis in labeling-based proteomics experiments. The original EBprot software employed a Gaussian mixture model to differentiate between differentially abundant proteins and nondifferentially abundant proteins based on log-transformed peptide-level ratios, assigning a probability score of differential abundance to each protein. This approach was based on the reproducible magnitude of peptide ratios. Still, it was somewhat limited by the inflexibility of its fully parametric model and the time-consuming nature of its R implementation, particularly for large datasets with over 100,000 peptides.

Addressing these limitations, EBprotV2 has been developed in the C++ programming language, offering significant improvements in computational efficiency. Additionally, it incorporates a flexible semiparametric model that is more adept at managing skewed ratio distributions, thus enhancing its analytical capabilities. This new version is not only faster but also more adaptable to the intricacies of proteomics data.

An essential feature of EBprotV2 is its integration with Perseus through a dedicated plugin, making it easily accessible to researchers using this popular data analysis framework. Furthermore, EBprotV2 introduces a new submodule, MakeGrpData, which is particularly innovative. This submodule converts label-free peptide intensity data into peptide ratio data, facilitating group comparisons and performing differential abundance analysis using mixture modeling. This feature is especially beneficial for datasets that contain many missing peptide intensity data points, offering a robust solution to a common challenge in proteomics data analysis.