Automated work-flow for processing high-resolution direct infusion electrospray ionization mass spectral fingerprints

Metabolomics

Volumn 3, Issue 1, 2007, Pages 41-54

  Hansen, Michael Adsetts Edberg ^a,b   Smedsgaard, Jørn ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Accurate mass; Data processing; Direct injection; Fungal extracts; Metabolomics; MS; Spectral library search; TOF

Indexed keywords

PENICILLIUM;

EID: 33947389136     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-006-0044-0     Document Type: Article

References (40)

1. Allen J., Davey H.M., Broadhurst D., Heald J.K., Rowland J.J., Oliver S.G., Kell D.B. (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat. Biotechnol. 21:692-696
2. Birkinshaw K. (2003) Deconvolution of mass spectra measured with a non-uniform detector array to give accurate ion abundances. J. Mass Spectrom. 38: 206-210
3. Crawford L.R., Morrison J.D. (1968) Computer methods in analytical mass spectrometry: Identification of an unknown compound in a catalog. Anal. Chem. 40:1464-1469
4. Fellenberg, K., Hauser, N.C., Brors, B., Neutzner, A., Hoheisel, J.D., Vingron, M. (2001). Correspondence analysis applied to microarray data, Proc. Natl. Acad. Sci. U.S.A. 98:10781-10786
5. Fiehn O. (2002) Metabolomics - the link between genotypes and phenotypes. Plant Mol. Biol. 48:155-171
6. Frisvad, J.C. and Samson, R.A. (2004). Polyphasic taxonomy of Penicillium subgenus Penicillium. A guide to identification of the food and air-borne terverticillate Penicillia and their mycotoxins. Stud. Mycol. 49
7. Gauss, K.F., "General Investigations of Curved Surfaces" [1827] and "New General Investigations of Curved Surfaces" [1825]. Both papers bound as one book, General Investigations of Curved Surfaces, trans. Adam Hiltebeitel and James Morehead, intro. by Richard Courant, Raven Press, Hewlett, New York, 1965
8. Greaves J. (2002) Operation of an academic open access mass spectrometry facility with particular reference to the analysis of synthetic compounds. J. Mass Spectrom. 37:777-785
9. Greenacre M., Hastie T. (1987) The geometric interpretation of correspondence analysis. J. Am. Stat. Assoc. 82:437-447
10. Grotch S.L. (1971) Computer techniques for identifying low resolution mass spectra. Anal. Chem. 43:1362-1370
11. Guilhaus M., Selby D.S., Mlynski V. (2000) Orthogonal acceleration time-of-flight mass spectrometry. Mass Spectrom. Rev. 19:65-107
12. Han X., Gross R.W. (2003) Global analysis of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: A bridge to lipodomics. J. Lipid Res. 44:1071-1079
13. Hansen M.E., Smedsgaard J. (2004) A new matching algorithm for accurate mass spectra. J. Am. Soc. Mass Spectrosc. 15:1173-2164
14. Hastie, T., Tibshirani, R., and Friedman, J. (2002). The elements of statistical learning; datamining, inference and prediction, Springer Verlag
15. Hertz H.S., Hites R.A., Biemann K. (1971) Identification of mass spectra by computer searching a file of known spectra. Anal. Chem. 43:681-691
16. Hill M.O. (1974) Correspondence analysis: A neglected multivariate method Appl. Stat. 23:340-354
17. Kell D.B. (2004) Metabolomics and system biology: Making sense of the soup. Curr. Opin. Biotechnol. 7:296-307
18. Krzanowski W.J. (1993) Attribute selection in correspondence analysis of incidence matrices, Appl. Stat. 42:529-541
19. Leow, W.K. and Li, R. (2001). Adaptive binning and dissimilarity measure for image retrieval and classification. In Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2, 234-239.
20. Leow, W.K. (2002). The algebra and analysis of adaptive-binning color histograms, Dept. of Computer Science, National University of Singapore, 3 Science Drive 2, Singapore 117543, Technical Report TRB8/02.
21. Maharjan R.P., Ferenci T. (2003) Global metabolite analysis: The influence of extraction methodology on metabolome profiles of Escherichia coli. Anal. Biochem. 313:145-154
22. Marchetti A.A., Mignerey A.C. (1993) Deconvolution of mass spectra. Nucl. Instrum. Methods Phys. Res. 324(1) 288-296
23. McLafferty F.W. (1974) Propability based matching of mass spectra. Org. Mass Spectrom. 9:690-702
24. Mead A. (1992) Review of the development of multidimensional scaling methods. The Statistician 41:27-39
25. Niessen W.M.A. (2003) Progress in liquid chromatography-mass spectrometry instrumentation and its impact on high-throughput screening. J. Chromatogr. A. 1000:413-436
26. Payne, T.R. and Edwards, P. (1999). Dimensionality reduction through correspondence analysis, The Robotics Institute, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburg PA 15232, USA, Tech. Rep. AUCS/ TR9910.
27. Pitt J.I. (1979) The Genus Penicillium and its Teleomorphic States Eupencillium and Taleromyces. Academic Press, London
28. Ramsay J.O. (1983) Some statistical approaches to multidimensional scaling data. J. Roy. Stat. Soc. A 145:285-312
29. Ripley B.D. (1996) Pattern Recognition and Neural Networks. Cambridge University Press, Cambridge
30. Roussopoulos, N., Kelley, S., and Vincent, F. (1995). Nearest neighbor queries, in Proceedings of the 1995 ACM-SIGMOD Intl. Conf. on Management of Data. 71-79
31. Samson R.A., Hoekstra E.S., Frisvad J.C., Filtenborg O. (2000) Introduction to Food and Airborne fungi, 6th ed. Centraalbureau voor Schimmelcultures, Utrecht
32. Smedsgaard J., Frisvad J.C. (1996) Using direct electrospray mass spectrometry in taxonomy and secondary metabolite profiling of crude fungal extracts. J. Microbiol. Meth. 25:5-17
33. Smedsgaard, J., A chemosystematic study of the terverticillate Penicillia using electrospray mass spectrometry, Ph.D. dissertation, IBT, Technical University of Denmark, Søltofts Plads, build 221, DK-2800 Kgs. Lyngby, 1996
34. Smedsgaard J. (1997a) Terverticillate Penicillia Studied by Direct Electrospray Mass Spectrometric Profiling of Crude Extracts. I. Chemosystematics. Biochem. Syst. Ecol. 25:51-64
35. Smedsgaard J. (1997b) Micro-scale extraction procedure for standardized screening of fungal metabolite production in cultures. J. Chromatogr. A 760:264-270
36. Smedsgaard, J., Hansen, M.E., and Frisvad, J.C. (2004). Classification of Terverticillate Penicillia by Electrospray Mass Spectrometric Profiling. Stud. Mycol. 49
37. Stein S.E., Scott D.R. (1994) Optimization and testing of mass spectral search algorithms for compound identification. J. Am. Soc. Mass Spectrosc. 5:859-866
38. Sumner L.W., Mendes P., Dixon R.A. (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics area. Phytochemistry 62:817-836
39. Vaidyanathan S., Kell D.B., Goodacre R. (2002) Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-thoughput bacteial identification. J. Am. Soc. Mass Spectrom. 13:118-128
40. Wehofsky M., Hoffmann R. (2002) Special feature: Perspective - automated deconvolution and deisotoping of electrospray mass spectra. J. Mass Spectrom. 37:223-229