Journal:OpenChrom: A cross-platform open source software for the mass spectrometric analysis of chromatographic data

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Full article title OpenChrom: A cross-platform open source software for the mass spectrometric analysis of chromatographic data
Journal BMC Bioinformatics
Author(s) Wenig, Philip; Odermatt, Juergen
Author affiliation(s) University of Hamburg
Primary contact Email: philip.wenig@gmx.net
Year published 2010
Volume and issue 11
Page(s) 405
DOI [1]
ISSN 1471-2105
Distribution license Creative Commons Attribution 2.0 Generic
Website http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-405
Download http://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-405 (PDF)
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Abstract

Background

Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform.

Results

This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported.

Conclusions

OpenChrom is a chromatography software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). There are no license constraints regarding extensions. They can be published using open source as well as proprietary licenses. OpenChrom is available free of charge at http://www.openchrom.net.

Background

Software has become an integral part of analysis techniques. Especially in the area of gas chromatography/mass spectrometry, automatic samplers enable high throughput analyses. Software assists handling large amounts of data generated by automated and fast operating analytical instruments. Modern computer systems are inexpensive, powerful and allow analysis techniques that could not have been applied in the past. Deconvolution, a chromatographic quality enhancing technique, demonstrates for instance that increasing processor power makes new analysis techniques applicable. The technique of deconvolution has been described by Biller and Biemann[1][2], Dromey et al.[3], Colby[4], Hindmarch et al.[5], Halket et al.[6], Kong et al.[7], Taylor et al.[8], Pool et al.[9][10] and Davies[11] in various ways. Stein[12] published an enhanced deconvolution algorithm that has been implemented in the software AMDIS (Automated Mass Spectral Deconvolution and Identification System).[13] AMDIS is available free of charge from the National Institute of Standards and Technology (NIST). Windig et al.[14][15] described another approach to enhance chromatographic quality by a deconvolution method called CODA (Component Detection Algorithm). The commercially available software ACD/MS Manager[16] offers an implementation of this approach.

References

  1. ↑ Biller, J.E.; Herlihy, W.C.; Biemann, K. (1977). "Identification of the components of complex mixtures by GC-MS". Abstracts Of Papers Of The American Chemical Society 173 (MAR20): 23–23. http://pubs.acs.org/doi/abs/10.1021/bk-1977-0054.ch002. 
  2. ↑ Biller, J.E.; Biemann, K. (1974). "Reconstructed Mass Spectra, A Novel Approach for the Utilization of Gas Chromatograph—Mass Spectrometer Data". Analytical Letters 7 (7): 515–528. doi:10.1080/00032717408058783. 
  3. ↑ Dromey, R.G.; Stefik, M.J.; Rindfleisch, T.C.; Duffield, A.M. (1976). "Extraction of mass spectra free of background and neighboring component contributions from gas chromatography/mass spectrometry data". Analytical Chemistry 48 (9): 1368–1375. doi:10.1021/ac50003a027. 
  4. ↑ Colby, B.N. (1992). "Spectral deconvolution for overlapping GC/MS components". Journal of the American Society for Mass Spectrometry 3 (5): 558–562. doi:10.1016/1044-0305(92)85033-G. PMID 24234499. 
  5. ↑ Hindmarch, P.; Demir, C.; Brereton, R.G. (1996). "Deconvolution and spectral clean-up of two-component mixtures by factor analysis of gas chromatographic–mass spectrometric data". Analyst 121 (8): 993-1001. doi:10.1039/AN9962100993. 
  6. ↑ Halket, J.M.; Przyborowska, A.; Stein, S.E. et al. (1999). "Deconvolution gas chromatography/mass spectrometry of urinary organic acids – potential for pattern recognition and automated identification of metabolic disorders". Rapid Communications In Mass Spectrometry 13 (4): 279–284. doi:10.1002/(SICI)1097-0231(19990228)13:4<279::AID-RCM478>3.0.CO;2-I. PMID 10097403. 
  7. ↑ Kong, H.W.; Ye, F.; Lu, X.; Guo, L.; Tian, J.; Xu, G.W. (2005). "Deconvolution of overlapped peaks based on the exponentially modified Gaussian model in comprehensive two-dimensional gas chromatography". Journal of Chromatography A 1086 (1–2): 160–164. doi:10.1016/j.chroma.2005.05.103. PMID 16130668. 
  8. ↑ Taylor, J.; Goodacre, R.; Wade, W.G. (1998). "The deconvolution of pyrolysis mass spectra using genetic programming: Application to the identification of some Eubacterium species". FEMS Microbiology Letters 160 (2): 237–246. doi:10.1111/j.1574-6968.1998.tb12917.x. PMID 9532743. 
  9. ↑ Pool, W.G.; deLeeuw, J.W.; vandeGraaf, B. (1996). "Backfolding applied to differential gas chromatography/mass spectrometry as a mathematical enhancement of chromatographic resolution". Journal Of Mass Spectrometry 31 (5): 509–516. doi:10.1002/(SICI)1096-9888(199605)31:5<509::AID-JMS323>3.0.CO;2-B. 
  10. ↑ Pool, W.G.; deLeeuw, J.W.; vandeGraaf, B. (1997). "Automated extraction of pure mass spectra from gas chromatographic/mass spectrometric data". Journal Of Mass Spectrometry 32 (4): 438–443. doi:10.1002/(SICI)1096-9888(199704)32:4<438::AID-JMS499>3.0.CO;2-N. 
  11. ↑ Davies, A. (1998). "The new Automated Mass Spectrometry Deconvolution and Identification System (AMDIS)". Spectrometry Europe 10 (3): 22–26. 
  12. ↑ Stein, S.E. (1999). "An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data". Journal Of the American Society for Mass Spectrometry 10 (8): 770–781. doi:10.1016/S1044-0305(99)00047-1. 
  13. ↑ "AMDIS". The National Institute of Standards and Technology. http://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:amdis. 
  14. ↑ Windig, W.; Smith, W.F. (2007). "Chemometric analysis of complex hyphenated data: Improvements of the component detection algorithm". Journal of Chromatography A 1158 (1–2): 251–257. doi:10.1016/j.chroma.2007.03.081. PMID 17418223. 
  15. ↑ Windig, W.; Phalp, J.M.; Payne, A.W. (1996). "A noise and background reduction method for component detection in liquid chromatography/mass spectrometry". Analytical Chemistry 68 (20): 3602–3606. doi:10.1021/ac960435y. 
  16. ↑ "ACD/Labs". Advanced Chemistry Development, Inc. http://www.acdlabs.com/. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. In the "Conclusion" section of the abstract, "software" was changed to "chromatography software" to encourage internal linking to the CDMS entry on the wiki.

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