Data Analysis ToolsKrönik is a command-line based application that reads Hardklör results and identifies the peptides that persist over several scans. This removes the redundancy in the results and helps identify "real" peptides in the data. The software is the same tool that was used to identify persistent peptide isotope distributions in the Hardklör publication.
Like Hardklör, Krönik is provided compiled for both Windows and GNU/Linux. You can download it from this link: Get Krönik now. Contact Mike MacCoss to request source code for Krönik.
File Format ToolsFor those who do not use a file format supported by Hardklör, we recommend the MS1 format:
McDonald,W.H. et al. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18, 2162-2168 (2004)
The MS1 file format is simple and easy to use, and is typically quicker to implement than complex XML data types. The format allows for easy conversion with most mass spec data. If you do not currently have software that can convert to mzXML, the MS1 format is the simplest approach.
For users of Xcalibur software, we provide MakeMS2, a simple Windows-based application to convert Xcalibur RAW files to MS1 or MS2 files using the XDK libraries. An indexer is also available upon request to speed the retrieval of data from these file. Contact Mike MacCoss to request source code for MakeMS2.
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.