EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data

We present EBprotV2,
a Perseus plugin for peptide-ratio-based differential
protein abundance analysis in labeling-based proteomics experiments.
The original version of EBprot models the distribution of log-transformed
peptide-level ratios as a Gaussian mixture of differentially abundant
proteins and nondifferentially abundant proteins and computes the
probability score of differential abundance for each protein based
on the reproducible magnitude of peptide ratios. However, the fully
parametric model can be inflexible, and its R implementation is time-consuming
for data sets containing a large number of peptides (e.g., >100 000).
The new tool built in the C++ language is not only faster in computation
time but also equipped with a flexible semiparametric model that handles
skewed ratio distributions better. We have also developed a Perseus
plugin for EBprotV2 for easy access to the tool. In addition, the
tool now offers a new submodule (MakeGrpData) to transform label-free
peptide intensity data into peptide ratio data for group comparisons
and performs differential abundance analysis using mixture modeling.
This approach is especially useful when the label-free data have many
missing peptide intensity data points.