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App: Hardklor Purpose: Analyze mass spectra Version History ------------------------------------------ 1.0 - Apr 17 2007 - Stable release 1.01 - May 17 2007 - Recompiled with latest MSToolkit(1.1) 1.02 - Jun 15 2007 - Fixed monoisotopic mass bug 1.03 - Aug 29 2007 - Added sensitivity level parameter - much better low abundance peptide performance. Some changes made to Mercury 1.1 - Sep 29 2007 - Added mzXML file support and compressed .cms1 & .cms2 support. Several bugfixes, including better S/N processing. 1.11 - Jan 16 2008 - Fixed bugs in MSToolkit 64-bit file support. Modified default Hardklor settings. 1.20 - Feb 6 2008 * Fixed user-defined scan window bug. * Allows reading of centroid data (-c). No signal-to-noise processing is done for this option. * Can set a static S/N cutoff for entire scan. This optimizes Orbitrap and LTQ-FT data analysis. See documentation. * Allows substitution of a user-defined molecule for averagine (-mol). Note: still in testing stages. * Toggle isotope distribution area for output in place of base isotope peak instensity (-da). * Minor speed improvements. 1.22 - Apr 24 2008 * Minor Bug Fixes * Upgraded MSToolkit software to 2.42 1.23 - Oct 24 2008 * Improvements to spectrum dividing functions 1.24 - Dec 11 2008 * Bugfixes for zoomscan and ultrazoomscan files 1.25 - Mar 3 2009 * Additional support for ms2 file format * Bugfix to MSToolkit (forked from SVN) 1.26 - Apr 30 2009 * Upgraded MSToolkit * Bugfix for rare S/N ratio calculation error * Potentially fixed rare, irregular, and odd 64-bit linux behavior 1.27 - Aug 13 2009 * Filenames and their paths can have spaces if entire path and filename is contained in quotes 1.28 - Sep 2 2009 * Writes results in XML format with the following parameter: -xml true 1.30 - Sep 13 2009 * Bugfix to QuickCharge algorithm 1.31 - Oct 1 2009 * Added new signal detection algorithm. It operates on the assumption valid signal peaks persist over multiple adjacent spectra. Detailed description of its usage can be found in the online documentation.