MSqRob Takes the Missing Hurdle: Uniting Intensity- and Count-Based Proteomics

Missing
values are a major issue in quantitative data-dependent
mass spectrometry-based proteomics. We therefore present an innovative
solution to this key issue by introducing a hurdle model, which is
a mixture between a binomial peptide count and a peptide intensity-based
model component. It enables dramatically enhanced quantification of
proteins with many missing values without having to resort to harmful
assumptions for missingness. We demonstrate the superior performance
of our method by comparing it with state-of-the-art methods in the
field.