Home Documentation Sample Config Files Tutorials Auxiliary Programs Download


Hardklör is a software application for the analysis of high- resolution mass spectra. It's primary function is the deconvolution and determination of monoisotopic mass and charge state of single and overlapping protein/peptide isotope distributions contained in a mass spectra.

In addition to Hardklör, several auxiliary utilities have been written to facilitate incorporation of Hardklör results into your experiments. Hardklör has been used to identify isotopically labeled species and make comparative quantitative analyses between multiple samples.

Contained within this website is the software, documentation, and examples of use necessary to set-up and run Hardklör from any desktop computer.

News & Updates

Apr 20, 2011: version 1.36 was released. Minor bugfixes were made when analyzing spectra on the highest sensitivity levels. Also, file support was updated to include the .mzML format. Jason Kwan from the University of Utah was kind enough to provide a binary for Mac OSx. The documentation on this site also looks a bit outdated, and I'll try to get on that soon.

Oct 19, 2010: version 1.34 was released. It was pointed out to me that this website was not being maintained, although development on Hardklör continues. I've thrown together a quick update and I'll notify the maintainers for future changes. In any case, so many changes have happened to Hardklör in the past two years that I can't possibly list them all here. It just works better.

July 10, 2008: version 1.22 was released. Minor bugfixes and file format updates. The documentation will be updated in the next week or so. For those who use compressed MS1 and MS2 data from MakeMS2, you will need to download the latest MakeMS2. Existing files converted to those formats will not work with this version.Auxiliary Programs.

January 11, 2008: The tutorial section on the web is completed. Krönik, a tool for identifying the persistent peptide isotope distributions from the Hardklör results was added to the Auxiliary Programs.

October 10, 2007: version 1.10 was released. Adds support for mzXML and compressed MS1 & MS2 files (see MakeMS2 in auxiliary programs). Additional bug fixes were made as well. The need for -txt flag has been removed. Tutorials to come soon.

September 17, 2007: Version 1.03 was released. It contains sensitivity improvements and minor bug fixes. Sensitivity can now be adjusted using the -sl tag. See the documentation for more information.


Hoopmann MR, Finney GL, MacCoss MJ, High speed data reduction, feature selection, and MS/MS spectrum quality assessment of shotgun proteomics datasets using high resolution mass spectrometry, Anal. Chem., 79, 5630-5632 (2007)

Hardklör is Copyright ©2007 University of Washington. All rights reserved. Written by Michael R. Hoopmann, Michael J. MacCoss, in the Department of Genome Sciences at the University of Washington.