OpenChrom
Encyclopedia
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.
) 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.
Open-source software
Open-source software is computer software that is available in source code form: the source code and certain other rights normally reserved for copyright holders are provided under a software license that permits users to study, change, improve and at times also to distribute the software.Open...
for the mass spectrometric
Mass spectrometry
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
analysis of chromatographic
Chromatography
Chromatography is the collective term for a set of laboratory techniques for the separation of mixtures....
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
Eclipse Public License
The Eclipse Public License is an open source software license used by the Eclipse Foundation for its software. It replaces the Common Public License and removes certain terms relating to litigations related to patents....
1.0 (EPL). Third-party libraries are separated into single bundles and are released under various OSI
Open Source Initiative
The Open Source Initiative is an organization dedicated to promoting open source software.The organization was founded in February 1998, by Bruce Perens and Eric S. Raymond, prompted by Netscape Communications Corporation publishing the source code for its flagship Netscape Communicator product...
compatible licenses.
History
OpenChrom was developed as a part of the PhD thesis by Philip Wenig (SCJP, LPIC-1Linux Professional Institute
The Linux Professional Institute Inc. is a non-profit organization that provides vendor-independent professional certification for Linux system administrators and programmers....
) 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
- http://sourceforge.net/projects/openchrom http://sourceforge.net/projects/openchrom OpenChrom at SourceForge
- http://www.openchrom.net http://www.openchrom.net OpenChrom Homepage
- Winner Eclipse Community Awards 2011 "Best RCP Application"
- Winner Thomas Krenn open source sponsorship 2010