In Journal of proteome research
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.
Kertesz-Farkas Attila, Nii Adoquaye Acquaye Frank Lawrence, Bhimani Kishankumar, Eng Jimmy K, Fondrie William E, Grant Charles, Hoopmann Michael R, Lin Andy, Lu Yang Y, Moritz Robert L, MacCoss Michael J, Noble William Stafford
2023-Jan-04
database search, false discovery rate control, mass spectrometry, open source software
