posted on 2023-01-04, 12:36authored byAttila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K. Eng, William E. Fondrie, Charles Grant, Michael R. Hoopmann, Andy Lin, Yang Y. Lu, Robert L. Moritz, Michael J. MacCoss, William Stafford Noble
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.