crux hardklor [options] <spectra>


Hardklör analyzes high-resolution mass spectra, identifying protein or peptide isotope distributions and determining the corresponding monoisotopic masses and charge states. The algorithm aims to identify persistence peptide isotope distribution (PPIDs), i.e., isotope distributions that recur over multiple scans. Hardklör is specifically designed to handle overlapping isotope distributions in a single spectrum. A detailed description of the Hardklör algorithm is given in

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



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: