OpenChrom

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OpenChrom
OpenChrom Logo.svg
Screenshot of OpenChrom Community Edition version 1.1.0 "Diels"
Screenshot of OpenChrom Community Edition version 1.1.0 "Diels"
Developer(s) Philip Wenig, Alexander Kerner, Lorenz Gerber, Matthias Mailänder, ...
Stable release
1.1.0 / August 1, 2016 (2016-08-01)
Written in Java[1]
Operating system Cross-platform
Type Chemoinformatics/Bioinformatics
License EPL, Third-party libraries under various OSI compatible licenses[2]
Website https://www.openchrom.net

OpenChrom is an open source software for the analysis and visualization of mass spectrometric and chromatographic data.[3] 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, macOS 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[edit]

ChemClipse version 0.7.0

OpenChrom was developed by Philip Wenig (SCJP, LPIC-1) as part of his PhD thesis at the University of Hamburg, Germany.[4] 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).[5][6]

OpenChrom won the Thomas Krenn Open Source Award 2010[7] as well as the Eclipse Community Award 2011.[8] The developers are also founding members of the Eclipse Science Working Group.[9] After successful commercialization of contract development and services around the OpenChrom project, vendor Lablicate reinforced the commitment to Free/Libre/Open-Source Software with the release of ChemClipse in October 2016, which serves as the base for all OpenChrom products.[10]

Supported data formats[edit]

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[edit]

  • 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[edit]

  • 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[edit]

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

Major features[edit]

OpenChrom offers a variety of features to analyze chromatographic data:

Releases[edit]

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 supported: 0.1.0
Goldstein Eugen Goldstein May 2010 Old version, no longer supported: 0.2.0
Wien Wilhelm Wien October 2010 Old version, no longer supported: 0.3.0
Tswett Mikhail Semyonovich Tswett April 2011 Old version, no longer supported: 0.4.0
Martin Archer John Porter Martin October 2011 Old version, no longer supported: 0.5.0
Synge Richard L. M. Synge April 2012 Old version, no longer supported: 0.6.0
Nernst Walther Nernst October 2012 Old version, no longer supported: 0.7.0
Dempster Arthur Jeffrey Dempster July 2013 Old version, no longer supported: 0.8.0
Mattauch Josef Mattauch July 2014 Old version, no longer supported: 0.9.0
Aston Francis William Aston July 2015 Old version, no longer supported: 1.0.0
Diels Otto Diels July 2016 Current stable version: 1.1.0
Alder Kurt Alder July 2017 Future release: 1.2.0
Legend:
Old version
Older version, still supported
Latest version
Latest preview version
Future release

Notes[edit]

  1. ^ The OpenChrom Open Source Project on Open Hub
  2. ^ Eclipse Marketplace: OpenChrom
  3. ^ 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
  4. ^ Softwarebasierte Verfahren zur datenbankgestützten Identifizierung organischer Substanzen mittels analytischer Pyrolyse gekoppelt mit Gaschromatographie/Massenspektrometrie (Py-GC/MS), Philip Wenig, Dissertation; 2012; Literature by and about OpenChrom in the German National Library catalogue
  5. ^ 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
  6. ^ 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
  7. ^ Werner Fischer: Winner Thomas Krenn Open Source Award 2010
  8. ^ Eclipse Foundation: Eclipse Community Awards Winners Announced, Santa Clara, CA - March 21, 2011
  9. ^ Diana Kupfer: Insight into the Eclipse Science Working Group, June 11, 2014
  10. ^ Philip Wenig: ChemClipse 0.7.0 released, October 2, 2016

External links[edit]