OpenChrom

OpenChrom

Developer(s)	Philip Wenig
Stable release	0.5.0 / October 30, 2011; 0 days ago (2011-10-30)
Written in	Java
Operating system	Cross-platform
Type	Chemoinformatics/Bioinformatics
License	EPL, Third-party libraries under various OSI compatible licenses
Website	[1] http://sourceforge.net/projects/openchrom

OpenChrom is an open source software for the mass spectrometric analysis of chromatographic data. Its focus is to handle native data files from several mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS). OpenChrom is able to import chromatographic data, such as (*.D) chromatograms from Agilent Technologies, Finnigan ITS40 (*.ms), NetCDF (*.cdf), MzXML (*.mzxml) and other formats. Moreover, it offers a nice and customizable graphical user interface. A basic set of methods to detect baselines and to detect and integrate peaks is provided. Preprocessing steps, for instance to remove certain mass fragments (m/z) such as nitrogen (28) or water (18), are supported by applying filter on the chromatogram or mass spectrum. Extensions are appreciated and can be easily integrated since OpenChrom is open source and uses a modular approach, which allows other developers to implement their own methods, algorithms, filters, detectors or integrators. Therefore, OpenChrom is an efficient system to process mass spectrometric, chromatographic data using an extensible and flexible plugin architecture.

OpenChrom is built on the Eclipse Rich Client Platform (RCP), hence it is available for various operating systems, e.g. Microsoft Windows, Linux and Mac OS X. It is distributed under the Eclipse Public License 1.0 (EPL). Third-party libraries are separated into single bundles and are released under various OSI compatible licenses.

History

OpenChrom was developed as a part of the PhD thesis by Philip Wenig (SCJP, LPIC-1) at the University of Hamburg, Germany. Philip was dissatisfied with the limitations of the available tools. Therefore he decided to implement a completely new approach, that offers modularity and flexibility needed in scientific research.

Major features

• Native handling of chromatographic data (Agilent *.D, Finnigan ITDS *.dat, Finnigan ITS40 *.ms, NetCDF *.cdf, mzXML *.mzxml, CSV *.csv)
• Export chromatographic data to Microsoft Office (Excel *.xlsx)
• Batch process support
• Baseline detector support
• Peak detector, integrator support
• Peaks and mass spectrum identifier support
• Filter support (e.g. Mass Fragment Removal, Noise Reduction, Savitzky-Golay Smoothing, CODA, Backfolding)
• Retention time shift support
• Chromatogram overlay mode
• Do/undo/redo support
• Integration of OpenOffice/LibreOffice and Microsoft Office
• Extensible by plugins

External links

• [2] http://sourceforge.net/projects/openchrom OpenChrom at SourceForge
• [3] http://www.openchrom.net OpenChrom Homepage
• Winner Eclipse Community Awards 2011 "Best RCP Application"
• Winner Thomas Krenn open source sponsorship 2010

References

• OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data, Philip Wenig, Juergen Odermatt, BMC Bioinformatics; 2010; www.biomedcentral.com/1471-2105/11/405/abstract
• Post-optimization of Py-GC/MS data: A case study using a new digital chemical noise reduction filter (NOISERA) to enhance the data quality utilizing OpenChrom mass spectrometric software, Philip Wenig, Journal of Analytical and Applied Pyrolysis; 2011; www.sciencedirect.com/science/article/pii/S0165237011001069