OpenChrom

OpenChrom

Screenshot of OpenChrom 0.8.0 "Dempster"
Developer(s)	Philip Wenig
Stable release	0.9.0 / August 5, 2014 (2014-08-05)
Written in	Java
Operating system	Cross-platform
Type	Chemoinformatics/Bioinformatics
License	EPL, Third-party libraries under various OSI compatible licenses
Website	http://www.openchrom.net

OpenChrom is an open source software for the analysis and visualization of mass spectrometric and 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), vendors like Agilent Technologies, Varian, Shimadzu, Thermo Fisher, PerkinElmer and others. But also data formats from other detector types are supported recently.

OpenChrom supports only the analysis and representation of chromatographic and mass spectrometric data. It has no capabilities for data acquisition or control of vendor hardware. OpenChrom is built on the Eclipse Rich Client Platform (RCP), hence it is available for various operating systems, e.g. Microsoft Windows, Mac OS X and Linux. 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 by Philip Wenig (SCJP, LPIC-1) as part of his PhD thesis at the University of Hamburg, Germany. The focus of the thesis was to apply pattern recognition techniques on datasets recorded by analytical pyrolysis coupled with chromatography and mass spectrometry (Py-GC/MS).

Supported data formats

Each system vendor stores the recorded analysis data in its own data format. These mass spectrometry data formats are most commonly proprietary. That makes it difficult to compare data sets from different systems and vendors. Furthermore, it's a big drawback for interlaboratory tests. The aim of OpenChrom is to support a wide range of different data formats natively. OpenChrom takes care that the raw data files can't be modified (see also Good laboratory practice). Hence, the raw data converters are not published under an open source license. The appropriate vendor converters can be installed from the OpenChrom marketplace. Their usage is free of charge. Moreover, OpenChrom supports several open formats to save the analysis results. In addition, OpenChrom offers its own open source format (*.ocb) that makes it possible to save the edited chromatogram as well as the peaks and identification results.

Mass selective detector

• Agilent *.D (DATA.MS and MSD1.MS)
• AMDIS Library (*.msl)
• Bruker Flex MALDI-MS (*.fid)
• Chromtech (*.dat)
• CSV (*.csv)
• Finnigan (*.RAW)
• Finnigan MAT95 (*.dat)
• Finnigan ITDS (*.DAT)
• Finnigan ITS40 (*.MS)
• JCAMP-DX (*.JDX)
• Microsoft Excel (*.xlsx)
• mzXML (*.mzXML)
• NetCDF (*.CDF)
• NIST Text (*.msp)
• OpenChrom XML (*.chrom)
• OpenChrom (*.ocb)
• Peak Loadings (*.mpl)
• PerkinElmer (*.raw)
• Varian SMS (*.SMS)
• Varian XMS (*.XMS)
• VG MassLab (*.DAT_001;1)
• Shimadzu (*.qgd)
• Shimadzu (*.spc)
• Waters (*.RAW)
• ZIP (*.zip)
• Agilent ICP-MS (*.icp)
• Finnigan ICIS (*.dat)
• mzML (*.mzML)
• SVG (*.svg)
• MassHunter (*.D)
• Finnigan ICIS (*.dat)
• MassLynx (*.RAW)

Flame ionization detector

• Agilent FID (*.D/*.ch)
• FID Text (*.xy)
• NetCDF (*.cdf)
• PerkinElmer (*.raw)
• Varian (*.run)
• Shimadzu (*.gcd)
• Arw (*.arw)

Other formats

• Peak Loadings (*.mpl)
• NIST-DB (*.msp)
• AMDIS (*.msl)
• AMDIS (*.cal)
• AMDIS (*.ELU)

Major features

OpenChrom offers a variety of features to analyze chromatographic data:

• Native handling of chromatographic data (MSD and FID)
• Batch process support
• Baseline detector support
• Peak detector, integrator support
• Peaks and mass spectrum identifier support
• Quantitation support
• Filter support (e.g. Mass Fragment and Scan Removal, noise reduction, Savitzky-Golay smoothing, CODA, backfolding)
• Retention time shift support
• Retention index support
• Chromatogram overlay mode
• Support for principal component analysis (PCA)
• Do/undo/redo support
• Integration of OpenOffice/LibreOffice and Microsoft Office
• Extensible by plug-ins
• Chromatogram and peak database support
• Update support
• Subtract mass spectra support

Releases

The software was first released in 2010. Each release is named after a famous scientist.

Notes

External links

• OpenChrom at SourceForge
• OpenChrom Homepage
• Winner Eclipse Community Awards 2011 "Best RCP Application"
• Winner Thomas Krenn open source sponsorship 2010
• Loads2Chrom

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
• Characterizing odorous emissions using new software for identifying peaks in chemometric models of gas chromatography – mass spectrometry datasets, K.R. Murphy, P. Wenig, G. Parcsi, T. Skov, R.M. Stuetz, Chemometrics and Intelligent Laboratory Systems; 2012; www.sciencedirect.com/science/article/pii/S0169743912001505
• Softwarebasierte Verfahren zur datenbankgestützten Identifizierung organischer Substanzen mittels analytischer Pyrolyse gekoppelt mit Gaschromatographie/Massenspektrometrie (Py-GC/MS), Philip Wenig, Dissertation; 2012; http://d-nb.info/gnd/1027167454