Jump to content

OpenChrom: Difference between revisions

Edit links
From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
No edit summary
No edit summary
Line 18: Line 18:
}}
}}


'''OpenChrom''' is an [[Open-source software|open source software]] for the analysis and visualization of [[Mass spectrometry|mass spectrometric]] and [[Chromatography|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|Agilent Technologies]], [[Varian Associates|Varian]], [[Shimadzu]], [[Thermo fisher|Thermo Fisher]], [[Perkin Elmer|PerkinElmer]] and others. But also data formats from other detector types are supported recently.
'''OpenChrom''' is an [[Open-source software|open source software]] for the analysis and visualization of [[Mass spectrometry|mass spectrometric]] and [[Chromatography|chromatographic]] data <ref>''OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data'', Philip Wenig, Juergen Odermatt, ''[[BMC Bioinformatics]]''; '''2010'''; {{DOI|10.1186/1471-2105-11-405}}</ref>. 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|Agilent Technologies]], [[Varian Associates|Varian]], [[Shimadzu]], [[Thermo fisher|Thermo Fisher]], [[Perkin Elmer|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_(software)#Rich_Client_Platform|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 [[Open Source Initiative|OSI]] compatible licenses.
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_(software)#Rich_Client_Platform|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 [[Open Source Initiative|OSI]] compatible licenses.


== History ==
== History ==
OpenChrom was developed by Philip Wenig ([[SCJP]], [[Linux Professional Institute|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).
OpenChrom was developed by Philip Wenig ([[SCJP]], [[Linux Professional Institute|LPIC-1]]) as part of his PhD thesis at the [[University of Hamburg]], Germany <ref>''Softwarebasierte Verfahren zur datenbankgestützten Identifizierung organischer Substanzen mittels analytischer Pyrolyse gekoppelt mit Gaschromatographie/Massenspektrometrie (Py-GC/MS)'', Philip Wenig, ''Dissertation''; '''2012'''; {{DNB|1027167454}}</ref>. 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) <ref>''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'''; {{DOI|10.1016/j.jaap.2011.05.013}}</ref><ref>''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'''; {{DOI|10.1016/j.chemolab.2012.07.006}}</ref>.

OpenChrom won the Thomas Krenn Open Source Award 2010 <ref>[http://www.thomas-krenn.com/de/wiki/Thomas_Krenn_Open_Source_F%C3%B6rderung_2010 Winner Thomas Krenn Open Source Award 2010]</ref><ref>[http://www.linux-magazin.de/NEWS/Preistraeger-fuer-Open-Source-Foerderung-stehen-fest Article in Linux Magazin]</ref> as well as the Eclipse Community Award 2011 <ref>[http://www.eclipse.org/org/press-release/20110321_awardwinners.php Sieger bei den Eclipse Community Awards 2011 „Best RCP Application“]</ref>.


== Supported data formats ==
== Supported data formats ==
Line 176: Line 178:


== References ==
== References ==
<references />
* ''OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data'', Philip Wenig, Juergen Odermatt, ''BMC Bioinformatics''; '''2010'''; [http://www.biomedcentral.com/1471-2105/11/405/abstract 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'''; [http://dx.doi.org/10.1016/j.jaap.2011.05.013 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'''; [http://dx.doi.org/10.1016/j.chemolab.2012.07.006 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 http://d-nb.info/gnd/1027167454]


[[Category:Bioinformatics software]]
[[Category:Bioinformatics software]]

Revision as of 08:38, 22 June 2015

OpenChrom
Developer(s)Philip Wenig
Stable release
0.9.0 / August 5, 2014 (2014-08-05)
Preview release
1.0.0-PREV / June 19, 2015 (2015-06-19)
Written inJava
Operating systemCross-platform
TypeChemoinformatics/Bioinformatics
LicenseEPL, Third-party libraries under various OSI compatible licenses
Websitehttp://www.openchrom.net

OpenChrom is an open source software for the analysis and visualization of mass spectrometric and chromatographic data [1]. 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 [2]. 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) [3][4].

OpenChrom won the Thomas Krenn Open Source Award 2010 [5][6] as well as the Eclipse Community Award 2011 [7].

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)
  • Finnigan Element II (*.dat)
  • 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)
  • Galactic Grams (*.cgm)

Flame ionization detector

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

Other formats

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

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.

Codename Eponym Date Version
Thomson Joseph John Thomson April 2010 Old version, no longer maintained: 0.1.0
Goldstein Eugen Goldstein May 2010 Old version, no longer maintained: 0.2.0
Wien Wilhelm Wien October 2010 Old version, no longer maintained: 0.3.0
Tswett Mikhail Semyonovich Tswett April 2011 Old version, no longer maintained: 0.4.0
Martin Archer John Porter Martin October 2011 Old version, no longer maintained: 0.5.0
Synge Richard L. M. Synge April 2012 Old version, no longer maintained: 0.6.0
Nernst Walther Nernst October 2012 Old version, no longer maintained: 0.7.0
Dempster Arthur Jeffrey Dempster July 2013 Old version, no longer maintained: 0.8.0
Mattauch Josef Mattauch July 2014 Current stable version: 0.9.0
Aston Francis William Aston July 2015 Latest preview version of a future release: 1.0.0
Legend:
Old version
Older version, still maintained
Latest version
Latest preview version
Future release

Notes

  1. ^ OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data, Philip Wenig, Juergen Odermatt, BMC Bioinformatics; 2010; doi:10.1186/1471-2105-11-405
  2. ^ Softwarebasierte Verfahren zur datenbankgestützten Identifizierung organischer Substanzen mittels analytischer Pyrolyse gekoppelt mit Gaschromatographie/Massenspektrometrie (Py-GC/MS), Philip Wenig, Dissertation; 2012;  This article incorporates text from a publication now in the public domain: Dictionary of National Biography. London: Smith, Elder & Co. 1885–1900. {{cite encyclopedia}}: Missing or empty |title= (help)
  3. ^ 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; doi:10.1016/j.jaap.2011.05.013
  4. ^ 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; doi:10.1016/j.chemolab.2012.07.006
  5. ^ Winner Thomas Krenn Open Source Award 2010
  6. ^ Article in Linux Magazin
  7. ^ Sieger bei den Eclipse Community Awards 2011 „Best RCP Application“

External links

References

Retrieved from "https://en.wikipedia.org/w/index.php?title=OpenChrom&oldid=668084125"