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In Bioinformatics (Oxford, England)

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 ( Source code is freely available from GitHub under the MIT license ( Support is provided via the GitHub issues tracker (

SUPPLEMENTARY INFORMATION : Supplementary data are available at Bioinformatics online.

Skinnider Michael A, Cai Charley, Stacey R Greg, Foster Leonard J