Abstract
We present a method for determining the sum formula of metabolites solely from their mass and isotope pattern. Metabolites, such as sugars or lipids, participate in almost all cellular processes, but the majority still remains uncharacterized. Our input is a measured isotope pattern from a high resolution mass spectrometer, and we want to find those molecules that best match this pattern.
Determination of the sum formula is a crucial step in the identification of an unknown metabolite, as it reduces its possible structures to a hopefully manageable set. Our method is computationally efficient, and first results on experimental data indicate good identification rates for chemical compounds up to 700 Dalton.
Above 1000 Dalton, the number of molecules with a certain mass increases rapidly. To efficiently analyze mass spectra of such molecules, we define several additive invariants extracted from the input and then propose to solve a joint decomposition problem.
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References
Audi, G., Wapstra, A., Thibault, C.: The AME2003 atomic mass evaluation (ii): Tables, graphs, and references. Nucl. Phys. A 729, 129–336 (2003)
Böcker, S., Lipták, Z.: Efficient mass decomposition. In: Proc. of ACM Symposium on Applied Computing (ACM SAC 2005), pp. 151–157 (2006)
Fürst, A., Clerc, J.-T., Pretsch, E.: A computer program for the computation of the molecular formula. Chemom. Intell. Lab. Syst. 5, 329–334 (1989)
Grange, A.H., Zumwalt, M.C., Sovocool, G.W.: Determination of ion and neutral loss compositions and deconvolution of product ion mass spectra using an orthogonal acceleration time-of-flight mass spectrometer and an ion correlation program. Rapid Commun. Mass Spectrom. 20(2), 89–102 (2006)
Hsu, C.S.: Diophantine approach to isotopic abundance calculations. Anal. Chem. 56(8), 1356–1361 (1984)
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M.: From genomics to chemical genomics: new developments in KEGG. Nuc. Acid Res. 34, D354–D357 (2006)
Kellerer, H., Pferschy, U., Pisinger, D.: Knapsack Problems. Springer, Heidelberg (2004)
Kubinyi, H.: Calculation of isotope distributions in mass spectrometry: A trivial solution for a non-trivial problem. Anal. Chim. Acta. 247, 107–119 (1991)
McLafferty, F.W.: Wiley Registry of Mass Spectral Data, 7th edn. with NIST 2005 spectral data edition. John Wiley & Sons, Chichester (2005)
Ojanperä, S., Pelander, A., Pelzing, M., Krebs, I., Vuori, E., Ojanperä, I.: Isotopic pattern and accurate mass determination in urine drug screening by liquid chromatography/time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom 20(7), 1161–1167 (2006)
Pellegrin, V.: Molecular formulas of organic compounds: the nitrogen rule and degree of unsaturation. J. Chem. Educ. 60(8), 626–633 (1983)
Rockwood, A.L., Van Orman, J.R., Dearden, D.V.: Isotopic compositions and accurate masses of single isotopic peaks. J. Am. Soc. Mass Spectr. 15, 12–21 (2004)
Wilf, H.: Generating Functionology. Academic Press, London (1990)
Yergey, J.A.: A general approach to calculating isotopic distributions for mass spectrometry. Int. J. Mass Spectrom. Ion Phys. 52(2-3), 337–349 (1983)
Zhang, N., Aebersold, R., Schwikowski, B.: ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2(10), 1406–1412 (2002)
Zhang, W., Chait, B.T.: ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 72(11), 2482–2489 (2000)
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Böcker, S., Letzel, M.C., Lipták, Z., Pervukhin, A. (2006). Decomposing Metabolomic Isotope Patterns. In: Bücher, P., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science(), vol 4175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11851561_2
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DOI: https://doi.org/10.1007/11851561_2
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