PeptideRanger: An R Package to Optimize Synthetic Peptide Selection for Mass Spectrometry Applications

Targeted and semitargeted mass spectrometry-based approaches are reliable methods to consistently detect and quantify low abundance proteins including proteins of clinical significance. Despite their potential, the development of targeted and semitargeted assays is time-consuming and often requires the purchase of costly libraries of synthetic peptides. To improve the efficiency of this rate-limiting step, we developed PeptideRanger, a tool to identify peptides from protein of interest with physiochemical properties that make them more likely to be suitable for mass spectrometry analysis. PeptideRanger is a flexible, extensively annotated, and intuitive R package that uses a random forest model trained on a diverse data set of thousands of MS experiments spanning a variety of sample types profiled with different chromatography setups and instruments. To support a variety of applications and to leverage rapidly growing public MS databases, PeptideRanger can readily be retrained with experiment-specific data sets and customized to prioritize and filter peptides based on selected properties.