Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra

Spectroscopy

Volumn 19, Issue 1, 2005, Pages 53-67

  Rousu, Juho ^a   Rantanen, Ari ^b   Ketola, Raimo A ^c   Kokkonen, Juha T ^c  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY OF HELSINKI   (Finland)

^c VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DISSOCIATION; FREQUENCIES; MASS SPECTROMETRY; REACTION KINETICS;

COLLISION ENERGY; GLYCINE; ISOTOPOMER DISTRIBUTIONS; ISOTOPOMERS;

ISOMERS;

ALANINE; AMINO ACID; ISOTOPE;

ACCURACY; ARTICLE; CHEMICAL REACTION; COLLISIONALLY ACTIVATED DISSOCIATION; FRAGMENTATION REACTION; MATHEMATICAL MODEL; SPECTROMETER; TANDEM MASS SPECTROMETRY; THEORETICAL STUDY;

EID: 12944292889     PISSN: 07124813     EISSN: None     Source Type: Journal    
DOI: 10.1155/2005/575686     Document Type: Article

References (26)

1. B. Christensen and J. Nielsen, Isotopomer analysis using GC-MS, Metabolic Engineering 1 (1999), E8-E16.
2. M. Dauner and U. Sauer, GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing, Biotechnology Progress 16 (2000), 642-649.
3. M. Dauner, J. Bailey and U. Sauer, Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis, Biotechnology and Bioengineering 76 (2001), 144-156.
4. 13C labeling pattern of glutamate, Journal of Biological Chemistry 268 (1993), 4170-4180.
5. New stable isotope-mass spectrometric techniques for measuring fluxes through intact metabolic pathways in mammalian systems: introduction of moving pictures into functional genomics and biochemical phenotyping, Metabolic Engineering 6(1) (2004), 85-100.
6. 13C isotopomer analysis of glutamate by tandem mass spec-trometry, Analytical Biochemistry 300 (2002), 102-205.
7. M. Klapa, S.M. Park, A.J. Sinskey and G. Stephanopoulos, Metabolite and isotopomer balancing in the analysis of metabolic cycles: I. Theory, Biotechnology and Bioengineering 62 (1999), 375-391.
8. W.-N. Lee, L.O. Byerley and E.A. Bergner, Mass isotopomer analysis: theoretical and practical considerations, Biological Mass Spectrometry 20 (1991), 451-458.
9. 13C labeling of common amino acids, European Journal of Biochemistry 268 (2001), 2464-2479.
10. A. Marx, A. de Graaf, W. Wiechert, L. Eggeling and H. Sahm, Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing, Biotechnology and Bioengineering 49 (1996), 111-129.
11. J.A. Morgan and D. Rhodes, Mathematical modeling of plant metabolic pathways, Metabolic Engineering 4(1) (2002), 80-89.
12. 13C-NMR/MS, Biotechnology and Bioengineering 68 (2000), 316-327.
13. G. Öz, P.G. Henry, E.R. Seaquist and R. Gruetter, Direct, noninvasive measurement of brain glycogen metabolism in humans, Neurochemistry International 43(4-5) (2000), 323-329.
14. S. Park, M. Klapa, A.J. Sinskey and G. Stephanopoulos, Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications, Biotechnology and Bioengineering 62 (1999), 392-401.
15. A. Rantanen, J. Rousu, R.A. Ketola, J.T. Kokkonen and V. Tarkiainen, Computing positional isotopomer distributions from tandem mass spectrometric data, Metabolic Engineering 4 (2002), 285-294.
16. J. Rousu, A. Rantanen, H. Maaheimo, E. Pitkänen, K. Saarela and E. Ukkonen, A method for estimating metabolic fluxes from incomplete isotopomer information. Proc. Computational Methods in Systems Biology (CMSB), Lecture Notes in Computer Science 2602 (2003), 88-103.
17. K. Schmidt, M. Carlsen, J. Nielsen and J. Villadsen, Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices, Biotechnology and Bioengineering 55 (1997), 831-840.
18. 13C coupling constraints on the isotopomer distribution in labeled biomass components, Metabolic Engineering 1 (1999), 166-179.
19. G. Stephanopoulos, A. Aristidou and J. Nielsen, Metabolic Engineering: Principles and Methodologies, Academic Press, 1998.
20. 13C labeling of proteinogenic amino acids. An efficient analytical tool to investigate intemediary metabolism, European Journal of Biochemistry 232 (1995), 433-448.
21. 13C labeling and two-dimensional NMR spectroscopy, Metabolic Engineering 1 (1999), 189-197.
22. W. Wiechert, M. Möllney, N. Isermann, M. Wurzel and A. de Graaf, Bidirectional steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems, Biotechnology and Bioengineering 66 (1999), 69-85.
23. W. van Winden, C. Wittman, E. Heinzle and J. Heijnen, Correcting mass isotopomer distributions for naturally occuring isotopes, Biotechnology and Bioengineenng 80 (2002), 477-479.
24. C. Wittmann and E. Heinzle, Mass spectrometry for metabolic flux analysis, Biotechnology and Bioengineering 62 (1999), 739-750.
25. C. Wittmann and E. Heinzle, Modeling and experimental design for metabolic flux analysis of lysine-producing corynebacteria by mass spectrometry, Metabolic Engineering 3 (2001), 173-191.
26. C. Zupke and G. Stephanopoulos, Modeling of isotope distributions and intracellular fluxes in metabolic networks using atom mapping matrices, Biotechnology Progress 10 (1994), 489-498.