OpenChrom
| OpenChrom
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 Screenshot of the OpenChrom Community Edition Version 1.3.0 "Dalton" |
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| Basic data
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| developer | Lablicate GmbH et al. |
| Current version | 1.4.0 (August 2019) |
| operating system | Windows , Mac OS X , GNU / Linux |
| programming language | Java |
| category | Chemo- and bioinformatics |
| License | EPL , third-party components partly under other OSI-compatible licenses |
| German speaking | No |
| openchrom.net | |
OpenChrom is free software for analyzing mass spectrometric data from chromatography . The focus is on the processing of measurement data from chromatographic systems (e.g. GC / MS, LC / MS, Py-GC / MS, HPLC-MS). Data formats from different manufacturers such as Agilent , Bruker , Shimadzu , Thermo Fisher Scientific , PerkinElmer and other providers are supported.
OpenChrom only supports the analysis of already recorded measurement data. Device control is not supported. The software has a customizable graphical user interface. Methods for finding baselines as well as detecting and integrating peaks are available for processing the chromatographic data. Filters allow additional optimization of the data, for example to remove mass fragments (m / z) such as water (18) and nitrogen (28). OpenChrom is free software and is based on a modular approach to integrate additional methods and algorithms into the platform. OpenChrom is based on the Eclipse Rich Client Platform (RCP) and is available for the Microsoft Windows, Linux and Mac OS X operating systems. OpenChrom is under the Eclipse Public License 1.0 (EPL). Third-party components are provided via separate plug-ins and are available under various OSI- compatible licenses.
history
OpenChrom was developed as part of Philip Wenig's dissertation at the University of Hamburg . In his work he dealt with pattern recognition on data from analytical pyrolysis coupled with gas chromatography and mass spectrometry (Py-GC / MS). Using the ChromIdent module, you can set up your own pyrogram databases for identification. The software was implemented generically accordingly, and it quickly became clear that the application could also be used for other issues with difficult-to-evaluate chromatograms, such as the analysis of odorous substances in a complex matrix.
In August 2010 OpenChrom took first place in the Thomas Krenn Open Source Funding Competition and in March 2011 it won the Eclipse Community Award for the best RCP application. The developers are also founding members of the Eclipse Science Working Group. Even after the successful commercialization of the free software and related services, the commitment of Lablicate in the area of open source was again confirmed by the publication of the sister software ChemClipse , whose naming rights are owned by the Eclipse Foundation .
The Lablicate team is integrated into research and teaching in the chemistry department at the University of Hamburg . Students interested in chemometrics and bioinformatics are specifically promoted and supported by mentoring . Through cooperation with the department for mass spectrometry , the OpenChrom developers stay in direct contact with the practitioners and their everyday usability problems in dealing with complex scientific evaluation software. In addition, the Lablicate team is also present at scientific events and offers workshops for young scientists .
Supported data formats
Each manufacturer usually stores the recorded measurement data in its own data format. In most cases, these data formats are proprietary and therefore inaccessible to software solutions from other manufacturers. A technically induced vendor lock-in leads to a distortion of competition . This makes the comparison of measurement data difficult and hinders scientific exchange. In addition, software developers have to carry out complex reverse engineering of the formats in order to make the data readable.
The goal of OpenChrom is to support the widest possible range of different formats. Converters integrated in the program are provided free of charge for this purpose . The raw data is imported and remains unchanged. In addition, OpenChrom enables the analyzed measurement data to be saved in open formats . OpenChrom provides its own open source format (* .ocb) for this purpose. This format not only saves the measurement data, but also the identification results.
Mass selective detector
- Agilent * .D (DATA.MS and MSD1.MS)
- AMDIS Library (* .msl)
- Bruker Flex MALDI-TOF 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)
Main functions
OpenChrom provides a large number of functions for processing chromatographic data, which are made available modularly through extensions ( plug-ins ) and can be imported and updated independently of the main program:
- native processing of chromatographic data ( MSD and FID )
- automatic processing of data ( batch processing )
- Baseline detection and correction
- Top Detectors and Integrators
- Filters (removal of mass fragments and scans, noise reduction, Savitzky-Golay filter , CODA , backfolding)
- Adjustment of retention times and setting of retention indices
- Comparison of chromatograms and identification of peaks and mass spectra to set up databases with reference substances
- Quantification with internal or external standards
- Subtraction of mass spectra
- Principal Component Analysis (PCA)
- Undo / redo functionality
- Integration of OpenOffice / LibreOffice and Microsoft Office
Versions
Official versions of OpenChrom have been available since 2010. Each version is named after a famous scientist in the field of chromatography and / or mass spectrometry.
| Project name | Namesake | date | version |
|---|---|---|---|
| Thomson | Joseph John Thomson | April 2010 | 0.1.0 |
| Goldstein | Eugen Goldstein | May 2010 | 0.2.0 |
| Vienna | Wilhelm Vienna | October 2010 | 0.3.0 |
| Tswett | Mikhail Semjonowitsch Zwet | April 2011 | 0.4.0 |
| Martin | Archer John Porter Martin | October 2011 | 0.5.0 |
| Synge | Richard LM Synge | April 2012 | 0.6.0 |
| Nernst | Walther Nernst | October 2012 | 0.7.0 |
| Dempster | Arthur Jeffrey Dempster | July 2013 | 0.8.0 |
| Matt also | Josef Mattauch | July 2014 | 0.9.0 |
| Aston | Francis William Aston | July 2015 | 1.0.0 |
| Diels | Otto Diels | July 2016 | 1.1.0 |
| Alder | Kurt Alder | August 2017 | 1.2.0 |
| Dalton | John Dalton | August 2018 | 1.3.0 |
| Lawrence | Ernest Lawrence | August 2019 | 1.4.0 |
Individual evidence
- ↑ Open Hub : OpenChrom Contributors: Listing
- ^ The OpenChrom Open Source Project on Open Hub
- ↑ OpenChrom in the Eclipse Marketplace
- ↑ Andreas Klingberg, Philip Wenig: Evaluate with Open Source. In: News from chemistry . 62, 2014, p. 1085, doi : 10.1002 / nadc.201490380 .
- ↑ Philip Wenig: OpenChrom - the cross-operating system open source alternative to ChemStation , July 10, 2012
- ↑ Software-based methods for the database-supported identification of organic substances using analytical pyrolysis coupled with gas chromatography / mass spectrometry (Py-GC / MS) , Philip Wenig, dissertation ; 2012 ; DNB 1027167454
- ↑ 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
- ↑ Dr. Philip Wenig, Dr. Andreas Klingberg: Using ChromIdent to evaluate pyrolysis GC / MS data - a sporting challenge , Lablicate UG September 11, 2014
- ↑ Characterizing odorous emissions using new software for identifying peaks in chemometric models of gas chromatography - mass spectrometry datasets , KR Murphy, P. Wenig, G. Parcsi, T. Skov, RM Stuetz, Chemometrics and Intelligent Laboratory Systems ; 2012 doi : 10.1016 / j.chemolab.2012.07.006 , Loads2Chrom
- ↑ Werner Fischer: Thomas Krenn Open Source Funding 2010 , Thomas-Krenn.AG, 23 Aug 2010
- ↑ Oliver Frommel: Award winners for open source funding have been selected , Admin-Magazin , 23 August 2010
- ↑ Alexander Neumann: EclipseCon: Eclipse Community Awards with German winners , Heise online , March 22, 2011
- ↑ Philip Wenig: Starting signal for the Eclipse Science Working Group , JAXenter, June 10, 2014
- ↑ Diana Kupfer: 'Open source and science are a dream team' , JAXenter, June 13, 2014
- ↑ Alexander Neumann: Developer tools for researchers under the umbrella of Eclipse , Heise online , June 24, 2014
- ↑ Hans-Joachim Baader: Eclipse starts science platform , Pro-Linux , June 24, 2014
- ↑ Philip Wenig: The time has come for a common, Eclipse-based platform for science , JAXenter, August 12, 2013
- ↑ Diana Kupfer: ChemClipse project: Eclipse for chemical analysis , JAXenter, January 5, 2015
- ↑ Hartmut Schlosser: ChemClipse introduces itself: Eclipse meets science , JAXenter, January 9, 2015
- ↑ Andreas Klingberg: Lablicate - A spin-off for analysis tools in the field of chromatography and mass spectrometry , CU, Chemistry, University of Hamburg , Die employee newspaper , issue 19, December 2015
- ↑ OpenChrom: Dr. M. Riedner / MS Department: Scientific Service: Organic Chemistry: Universität Hamburg ( Memento of the original from November 7, 2017 in the Internet Archive ) Info: The archive link has been inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice.
- ↑ Philip Wenig, Andreas Klingberg: Processing and interpretation of mass spectrometric data with OpenChrom , German Society for Mass Spectrometry
literature
- 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