ProteoForge is out in Journal of Proteome Research. What changed during review, what is still broken, and where the package is headed.

The story behind ProteoForge, a framework for finding differential proteoforms in bottom-up proteomics data. Why protein-level averages hide biology, how missing data broke every tool we tried, and what we found when we applied it to a hypoxia dataset.

Probabilistic dropout analysis for label-free proteomics. Handles missing values by modeling dropout curves instead of imputing.