SUMMARY: We present PrInCE, an R/Bioconductor package that employs a machine-learning approach to infer protein-protein interaction networks from co-fractionation mass spectrometry (CF-MS) data. Previously distributed as a collection of Matlab scripts, our ground-up rewrite of this software package in an open-source language dramatically improves runtime and memory requirements. We describe several new features in the R implementation, including a test for the detection of co-eluting protein complexes and a method for differential network analysis. PrInCE is extensively documented and fully compatible with Bioconductor classes, ensuring it can fit seamlessly into existing proteomics workflows. AVAILABILITY AND IMPLEMENTATION: PrInCE is available from Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/PrInCE.html). Source code is freely available from GitHub under the MIT license (https://github.com/fosterlab/PrInCE). Support is provided via the GitHub issues tracker (https://github.com/fosterlab/PrInCE/issues). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.