The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data

The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive summary has not been published since 2014. The goal of this work is to summarize the functionality of Crux, focusing on developments since 2014. We begin with empirical results demonstrating our recently implemented speedups to the Tide search engine. Other new features include a new score function in Tide, two new confidence estimation procedures, as well as three new tools: Param-medic for estimating search parameters directly from mass spectrometry data, Kojak for searching cross linked mass spectra, and DIAmeter for searching data independent acquisition data against a sequence database.

Automated summary

The Crux tandem mass spectrometry data analysis toolkit is a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Although many publications have described the individual components of Crux, a comprehensive summary has not been published since 2014. The goal of this work is to provide a summary of Crux's functionality, focusing on developments since 2014. Recent developments include speed improvements to the Tide search engine, a new score function, two new confidence estimation procedures, and three new tools.