OpenChrom

OpenChrom
	Screenshot of OpenChrom version 1.5.0 "McLafferty"
Developer(s)	Lablicate & Scientific community
Stable release	1.5.0 (rolling)
Written in	Java
Operating system	Cross-platform
Type	Chemoinformatics/Bioinformatics
License	EPL, Third-party libraries under various OSI compatible licenses
Website	https://www.openchrom.net

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

OpenChrom was developed by Philip Wenig as part of his PhD thesis at the University of Hamburg, Germany.^[5] 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).^[6]^[7]

OpenChrom won the Thomas Krenn Open Source Award 2010^[8] as well as the Eclipse Community Award 2011.^[9] The developers are also founding members of the Eclipse Science Working Group.^[10] 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.^[11]

Supported data formats

Each system vendor stores the recorded analysis data in its own proprietary format. 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 mass spectrometry data formats natively.^[12] OpenChrom takes care that the raw data files can't be modified according to the good laboratory practice. To help scientists OpenChrom supports several open formats to import and export 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 ChemStation *.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)
mzData (*.mzData)
NetCDF (*.CDF)
NIST Text (*.msp)
Open Chromatography Binary (*.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)
mzMLb (*.mzMLb)
mz5 (*.mz5)
mzDB (*.mzDB)
SVG (*.svg)
MassHunter (*.D)
Finnigan ICIS (*.dat)
MassLynx (*.RAW)
Galactic Grams (*.cgm)
AnIML (*.animl)
GAML (*.gaml)
...

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)
AnIML (*.animl)
GAML (*.gaml)
...

Diode-array detection

Agilent DAD (*.UV/*.ch)
ABSciex
Chromulan
Shimadzu (*.lcd)
Waters Empower
AnIML (*.animl)

Fourier-transform infrared spectroscopy

Thermo Galactics (*.spc)
Thermo Fisher Nicolet (*.spa)
GAML (*.gaml)

Near-infrared spectroscopy

Bruker OPUS (*.0)

Other formats

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

Major features

OpenChrom offers a variety of features to analyze chromatographic data:

Native handling of chromatographic data (MSD and FID)
Batch processing support
Baseline detector support
Peak detector, integrator support
Peak deconvolution
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 peak pattern analysis
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	Old version, no longer maintained: 0.9.0
Aston	Francis William Aston	July 2015	Old version, no longer maintained: 1.0.0
Diels	Otto Diels	July 2016	Old version, no longer maintained: 1.1.0
Alder	Kurt Alder	August 2017	Old version, no longer maintained: 1.2.0
Dalton	John Dalton	August 2018	Old version, no longer maintained: 1.3.0
Lawrence	Ernest Lawrence	August 2019	Old version, no longer maintained: 1.4.0
McLafferty	Fred McLafferty	March 2022	Current stable version: 1.5.0^{[note 1]}

Old version

Older version, still maintained

Latest version

Future release

^ Rolling Release from here. Only the timestamp changes.

References

^ OpenChrom Contributors, Black Duck OpenHub
^ The OpenChrom Open Source Project on Open Hub
^ Eclipse Marketplace: OpenChrom
^ 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
^ Softwarebasierte Verfahren zur datenbankgestützten Identifizierung organischer Substanzen mittels analytischer Pyrolyse gekoppelt mit Gaschromatographie/Massenspektrometrie (Py-GC/MS), Philip Wenig, Dissertation; 2012; DNB-IDN 1027167683
^ 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
^ 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
^ Werner Fischer: Winner Thomas Krenn Open Source Award 2010
^ Eclipse Foundation: Eclipse Community Awards Winners Announced, Santa Clara, CA - March 21, 2011
^ Diana Kupfer: Insight into the Eclipse Science Working Group, June 11, 2014
^ Philip Wenig: ChemClipse 0.7.0 released, October 2, 2016
^ Dąbrowski, Łukasz (2015-08-07). "Review of free data processing software for chromatography". Mediterranean Journal of Chemistry. 4 (4): 193–200. doi:10.13171/mjc.4.4.2015.15.09.16.35/dabrowski.