Release notes for Crux

Version 4.3

March 25, 2025

Major changes

  • 19 March 2025: Updated to use Comet 2025.01.1, including support for indexing a sequence database.
  • 11 December 2024: Updated to use Percolator rel 3-07-01. Retention time now included in Percolator output.
  • 18 Oct 2024: speeded up tide-search, restuctured its code.
  • 18 Oct 2024: Added support to produce output in mztab format.
  • 18 Oct 2024: tide-index supports unimod codes.

    Minor changes

  • 24 March 2025: Fixed issue #696 failure in pipeline application.
  • 14 Feb 2025: Improved tide-search run time.
  • 6 Feb 2025: create Spectrum Convert application.
  • 28 Jan 2025: Bug fix in tide-search when searching without decoy peptides.
  • 25 Oct 2024: Fixed bug in parameter handling for spectral-counts inside of the pipeline command.
  • 25 Oct 2024: add .gz format as read fasta file option.
  • 22 Oct 2024: added error message when user specifies non-supported score functions. fixed bug that prevented building on windows/mac.
  • 18 Oct 2024: terminal amino acids can be modified by terminal modifications and resiudal mods.
  • 18 Oct 2024: tide-search reports tailor scores, and statistics about b-y- ions.
  • 18 Oct 2024: tide-search runs only combined p-values.
  • 18 Oct 2024: non-used options removed from tide-search: --compute-sp, --file-column, --brief-output, --peptide-centric-search, --evidence-granularity, --use-tailor-calibration (it is automatically calculated), From tide-index:--keep-terminal-aminos.
  • 15 September 2024: Unify Sorting. Replace quick sort algorithms with std::sort
  • 11 September 2024: Removed usage plot from Crux website home page.
  • 06 Auguest 2024: Minor changes to website support.
  • 30 July 2024: Modified tool use events to submit via GA4.
  • 02 July 2024: Typo fix in the documentation of precursor window calculation.
  • Version 4.2

    April 6, 2024

    Major changes

  • 6 April 2024: Updated to use Percolator commit d0d48b5.
  • 11 March 2024: Updated to use ProteoWizard 3.0.24044.fd6604. This required shifting Crux and dependencies to the C++14 standard and disabling the C++11 ABI. This fixed issues building Crux on newer releases of Linux and MacOS. The Centos 7 build was replaced with Ubuntu 20.04 in GitHub commit action for Master branch. The recommended version of CMake is now 3.24. Earlier versions will work, but you may see some warning messages.
  • Minor changes


    Version 4.1

    October Oct. 11, 2021

    Major changes

    Minor changes


    Version 4.0

    April 06, 2021

    Major changes

    Minor changes


    Version 3.2.x

    June 19, 2018

    Major changes

    Minor changes

    Version 3.2

    May 20, 2018

    Major changes

    Minor changes


    Version 3.1

    January 10, 2017

    Major changes

    Minor changes


    Version 3.0

    August 1, 2016

    Major changes

    Minor changes


    Version 2.1

    October 8, 2014

    Major enhancements

    Minor changes


    Version 2.0

    June 6, 2014

    Major enhancements

    Minor changes


    Version 1.40

    May 22, 2013

    Major enchancements

    Minor changes


    Version 1.39

    October 6, 2012

    Major enchancements

    Minor changes


    Version 1.38

    July 20, 2012

    Major enhancements

    Minor changes


    Version 1.37

    December 22, 2011

    Major enhancements

    Minor changes


    Version 1.36

    August 4, 2011

    Tide changes

    Minor changes


    Version 1.35

    March 23, 2011

    Major enhancements

    Minor changes


    Version 1.34

    December 22, 2010

    Minor changes


    Version 1.33

    July 7, 2010

    Major enhancements

    Minor changes


    Version 1.32

    July 6, 2010

    Major enhancement

    Minor changes


    Version 1.31

    June 2, 2010

    Major enhancements

    Minor changes


    Version 1.30

    May 5, 2010

    Major enhancements

    Minor changes


    Version 1.22

    September 16, 2009

    Major enhancements

    Minor changes


    Version 1.21

    May 14, 2009

    Version 1.20

    January 6, 2009

    Version 1.02

    December 1, 2008

    Version 1.01

    October 15, 2008


    Version 1.0

    March 4, 2008

    Initial release