OpenChrom – Wikipedia

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OpenChrom
OpenChrom Logo.svg
OpenChrom 1.5.0.png
OpenChrom Version 1.5.0 „McLafferty“
Will be base data
developer Lablicate GmbH et al. [first]
Publishing year March 24, 2010 [2]
Current version 1.5.0
( March 25, 2022 )
operating system Microsoft Windows, macOS, Linux
programming language Java [3]
Category Chemical and bioinformatics
License EPL, third components partly among other OSI-compatible licenses [4]
German -speaking no
OpenCHROM.NET

OpenChrom is free software for analyzing mass spectrometric data of chromatography. The focus is on the processing of measurement data of chromatographic systems (e.g. GC/MS, LC/MS, PY-GC/MS, HPLC-MS). Data formats of different manufacturers such as agile, Bruker, Shimadzu, Thermo Fisher Scientific, Perkinelmer and other providers are supported. [5]

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Openchrome only supports the analysis of already recorded measurement data. A device control is not supported. The software has a customizable graphic surface. Methods for finding basic lines as well as for detecting and integrating tips are available for editing the chromatographic data. Filter allow additional optimization of the data, for example to remove mass fragments (m/z) such as water (18) and nitrogen (28). [6] Openchrome is free software and is based on a modular approach to integrate additional methods and algorithms into the platform. Openchrom builds on the Eclipse Rich Client Platform (RCP) and is available for the Microsoft Windows, Linux and Mac OS X operating systems. Openchrome is under the Eclipse Public License 1.0 (EPL). Third components are provided via separate plugins and are available under various OSI-compatible licenses.

ChemClipse in Version 0.7.0

Openchrome was created as part of Philip’s dissertation at the University of Hamburg. [7] In his work, he dealt with pattern recognition to data from analytical pyrolysis coupled with gas chromatography and mass spectrometry (PY-GC/MS). [8] Using the Chromident module, own pyrogram databases can be built up for identification. [9] The software was implemented accordingly, and it quickly became clear that the application can also be applied to other questions with difficult to evaluate chromatograms such as the analysis of odoral substances in a complex matrix. [ten]

In August 2010, Openchrom took first place at Thomas Kren’s open source promotion competition [11] [twelfth] as well as the Eclipse Community Award won the Eclipse Community Award as the best RCP application. [13] The developers are also founding members of the Eclipse Science Working Group. [14] [15] [16] [17] [18] Even after the successful commercialization of the free software and associated services, the commitment of the Lablicate company in the area of ​​open source by publishing the sister software ChemClipse , whose name rights bear the Eclipse Foundation, confirmed again. [19] [20]

The Lablicate team is integrated into research and teaching in the Chemistry Department of the University of Hamburg. Interested students are specifically encouraged and supported by mentoring in chemometric and bioinformatics. [21] Through cooperation with the department for mass spectrometry, the openchrome developers remain in direct contact with the practitioners and their everyday usability problems in dealing with complex scientific evaluation. [22] In addition, the Lablicate team is also present at scientific events and offers workshops for young scientists. [23]

Each manufacturer usually uses the measured measurement data in its own data format. In most cases, these data formats are proprietary and thus inaccessible to software solutions from other manufacturers. There is a distortion of competition through a technically brought about Vendor-Lock-in. This makes the comparison of measurement data difficult and hinders the scientific exchange. In addition, software developers have to carry out complex reverse engineering of the formats in order to make the data legible.

Openchrome’s goal is to support the largest possible range of different formats. For this purpose, integrated converters are made available free of charge in the program. The raw data are imported and remain unchanged. In addition, Openchrome enables the analyzed measurement data to be saved in open formats. For this purpose, Openchrome provides its own open source format (*.ocb). This format not only stores the measurement data, but also the identification results.

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Massenate selectives detector [ Edit | Edit the source text ]

  • Agilent *.D (DATA.MS and MSD1.MS)
  • AMDIS Library (*.msl)
  • Bruker Flex MALDI-TOF MS (*.fid)
  • Chromech (* .dat)
  • CSV (* .CSV)
  • Finnigan (*.RAW)
  • Finnigan Mat95 (*. Dat)
  • Finnigan Its (* .dat)
  • Finnigan ITS40 (*.MS)
  • Finnigan Element ii (*.DAT)
  • JCAMP-DX (*.JDX)
  • Microsoft Excel (*.xlsx)
  • mzxml (*.mzxml)
  • mzdata (*.mzdata)
  • NetCDF/ANDI/AIA (*.cdf)
  • NIST Text (*.msp)
  • OpenChrom (*.ocb)
  • Peak Loadings (*.mpl)
  • PerkinElmer (*.raw)
  • SMS variant (*.SMS)
  • Varian XMS (*.XMS)
  • VG Masslab (*. Dat_001; 1)
  • Shimadzu (*.qgd)
  • Shimadzu (*.spc)
  • Waters (*.RAW)
  • Agilent ICP-MS (*.icp)
  • Finnigan ICIS (* .dat)
  • mzml (* .mzml)
  • mzmlb (*.mzmlb)
  • MZ5 (*.MZ5)
  • mzDB (*.mzDB)
  • MassHunter (*.D)
  • Finnigan ICIS (* .dat)
  • MassLynx (*.RAW)
  • Galactic Grams (*.cgm)
  • GAML (*.gaml)
  • Mascot Generic Format (*.mgf)
  • Animl
  • …

Flame ionization detector [ Edit | Edit the source text ]

  • Agilent FID (*.D/*.ch)
  • FID Text (*.xy)
  • NetCDF/ANDI/AIA (*.cdf)
  • PerkinElmer (*.raw)
  • Varian (*.run)
  • Finnigan Fid (* .dat)
  • Finnigan FID (*.raw)
  • Shimadzu (*.gcd)
  • Arw (*.Arw)
  • GAML (*.gaml)
  • Animl (* .Animl)
  • Thermo Scientific Atlas (*.r01)
  • Points (*.chr)
  • …

Diodearaydetector [ Edit | Edit the source text ]

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

FT-IR [ Edit | Edit the source text ]

  • JCAMP-DX (*.dx)
  • Thermo Galactics (*.spc)
  • Thermo Fisher Nicolet (*.spa)
  • GAML (*.gaml)

NIR [ Edit | Edit the source text ]

Further formats [ Edit | Edit the source text ]

  • Peak Loadings (*.mpl)
  • NIST-DB (*.msp)
  • Amdis library (*.msl)
  • AMDIS Kalibrierstandard (*.cal)
  • Amdi’s result file (*.elu)
  • MassBank (*.txt)
  • SVG (*.SVG)
  • ZIP (*.zip)
  • Sirius database (*.ms)
  • HPTCLCBAB

Openchrome provides a variety of functions for editing chromatographic data that are made available modularly by extensions (plug-ins) and can be recorded and updated regardless of the main program:

There have been official versions of Openchrom since 2010. Each version is named after a famous scientist from the field of chromatography and/or mass spectrometry.

Legend:

Older version; no longer supported

Older version; still supported

Current version

Current Vorab version

Future version

* From this version continuous publication (Rolling release) Only the date stamp changes

  1. ↑ Open Hub: OpenChrom Contributors: Listing
  2. ↑ OpenChrom Release 0.1.0 on SourceForge .
  3. ↑ The openchrom Open Source Project on Open Hub: Languages Page . In: Open Hub . (accessed on July 19, 2018).
  4. ↑ OpenChrom im Eclipse Marketplace
  5. ↑ Andreas Klingberg, Philip little: Evaluate with open source. In: Messages from the chemistry. 62, 2014, S. 1085, two: 10.1002 / NADC.201490380 .
  6. ↑ a b c Philip little: Openchrome-The cross-operating system open-source alternative to the chem station ( PDF ), July 10, 2012
  7. ↑ Software-based methods for database-based identification of organic substances coupled using analytical pyrolysis coupled with gas chromatography/mass spectrometry (PY-GC/MS) , Philip little, Dissertation ; 2012 ; DNB 1027167683
  8. ↑ 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 little, Journal of Analytical and Applied Pyrolysis ; 2011 ; doi: 10.1016/j.jaap.2011.05.013 .
  9. ↑ Dr. Philip Little, Dr. Andreas Klingberg: Using the chromident evaluation of pyrolysis GC/MS data-a sporting challenge , Lablicate and 11. September 2014.
  10. ↑ 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 , Loads2Chrom .
  11. ↑ Werner Fischer: Thomas Krenn Open Source Funding 2010 , Thomas-Krenn.AG, 23. Aug. 2010.
  12. ↑ Oliver crumpled: Prize winners for open source funding have been determined , Admin-Magazin, 23. August 2010.
  13. ↑ Alexander Neumann: ECLIPSECON: Eclipse Community Awards with German winners , Heise Online, March 22, 2011.
  14. ↑ Philip little: The starting signal for the Eclipse Science Working Group , Jaxents, June 10, 2014
  15. ↑ Diana copper: ‘Open source and science are a Dream team’ , Jaxents, June 13, 2014.
  16. ↑ Alexander Neumann: Developer tools for researchers under the roof of Eclipse , Heise Online, June 24, 2014
  17. ↑ Hans-Joachim Baader: Eclipse starts science platform , Pro-Linux, June 24, 2014.
  18. ↑ Philip little: Time is ripe for a common, Eclipse-based platform for science , JAXenter, 12. August 2013.
  19. ↑ Diana copper: Project Chemclipse: Eclipse for chemical analysis , Jaxents, 5. January 2015.
  20. ↑ Hartmut Schlosser: Chemclipse imagines: Eclipse meets science , Jaxenter, 9. January 2015.
  21. ↑ Andreas Klingberg: Lablicate – a spin -off for analysis tools in the field of chromatography and mass spectrometry , Cu, chemistry, university Hamburg, the employee newspaper, issue 19, December 2015.
  22. ↑ University of Hamburg: Department of Chemistry: Openchrom® .
  23. ↑ Philip Little, Andreas Klingberg: Processing and interpretation of mass -spectrometric data with openchrome , German Society for Mass Spectrometry.
  24. ↑ Eclipse for chemists: Openchrom 0.8.0 with many innovations
  25. ↑ Freshly cleaned for chemical analysis: open chrome 0.8.0
  26. ↑ Eclipse software Openchrome with new data converters
  27. ↑ Openchrome 1.0.0 with new data converters

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