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An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data


A method is presented for extracting individual component spectra from gas chromatography/mass spectrometry (GC/MS) data files and then using these spectra to identify target compounds by matching spectra in a reference library. It extends a published “model peak” approach which uses selected ion chromatograms as models for component shape. On the basis of this shape, individual mass spectral peak abundance profiles are extracted to produce a “purified” spectrum. In the present work, ion-counting noise is explicitly treated and a number of characteristic features of GC/MS data are taken into account. This allows spectrum extraction to be reliably performed down to very low signal levels and for overlapping components. A spectrum match factor for compound identification is developed that incorporates a number of new corrections, some of which employ information derived from chromatographic behavior. Test results suggest that the ability of this system to identify compounds is comparable to that of conventional analysis.

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  1. Biller, J. E.; Biemann, K. Reconstructed mass spectra, a novel approach for the utilization of gas chromatograph—mass spectrometer data. Anal. Lett. 1974, 7, 515–528.

    CAS  Google Scholar 

  2. Colby, B. N. Spectral deconvolution for overlapping GC/MS components J. Am. Soc. Mass Spectrom. 1992, 3, 558–562.

    Article  CAS  Google Scholar 

  3. Herron, N. R.; Donnelly, J. R.; Sovocool, G. W. Software-based mass spectral enhancement to remove interferences from spectra of unknowns. J. Am. Soc. Mass Spectrom. 1996, 7, 598–604.

    Article  CAS  Google Scholar 

  4. Pool, W. G.; Leeuw, J. W.; van de Graaf, B. Automated extraction of pure mass spectra from gas chromatographic/mass spectrometric data. J. Mass Spectrom. 1997, 32, 438–443.

    Article  CAS  Google Scholar 

  5. Dromey, R. G.; Stefik, M. J.; Rindfleisch, T. C.; Duffield, A. M. Extraction of mass spectra free of background and neighboring component contributions from gas chromatography/mass spectrometry data. Anal. Chem. 1976, 48, 1368–1375.

    Article  CAS  Google Scholar 

  6. Shackelford, W. M.; Cline, D. M.; Faas, L.; Kurth, G. An evaluation of automated spectrum matching for survey identification of wastewater components by gas chromatography-mass spectrometry. Anal. Chim. Acta 1983, 146, 25–27.

    Article  Google Scholar 

  7. Hargrove, W. F.; Rosenthal, D.; Cooley, P. C. Improvement of algorithm for peak detection in automatic gas chromatography-mass spectrometry data processing. Anal. Chem. 1981, 53, 538–539.

    Article  CAS  Google Scholar 

  8. Karjalainen, E. J.; Karjalainen, U. P. Data Analysis for Hyphenated Techniques. Elsevier: Amsterdam, 1996.

    Google Scholar 

  9. Stein, S. E.; Scott, D. R. Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 1994, 5, 859–866.

    Article  CAS  Google Scholar 

  10. Peterson, D. W.; Hayes, J. M. Signal-to-noise ratios in mass spectroscopic ion-current-measurement systems. In Contemporary Topics in Analytical and Clinical Chemistry; Plenum: New York, 1978, Vol 3, 217–251.

    Google Scholar 

  11. Standard Reference Data Program, National Institute of Standards and Technology, Gaithersburg, MD. Standard Reference Database IA. Internet address:

  12. Halket, J. M.; Przyborowska, A.; Stein, S. E.; Mallard, W. G.; Down, S.; Chalmers, R. A. Deconvolution GC/MS of urinary organic acids—Potential for pattern recognition for automated identification of metabolic disorders Rapid Commun. Mass Spectrom. 1999, 13, 279–284.

    Article  CAS  Google Scholar 

  13. Davies, T. The new automated mass spectrometry deconvolution and identification system (AMDIS). Spectrosc. Eur. 1998, 10/3, 24–27.

    Google Scholar 

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Stein, S.E. An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J Am Soc Mass Spectrom 10, 770–781 (1999).

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