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Volume 19 (2005), Issue 1, Pages 53-67

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

Juho Rousu,1,4 Ari Rantanen,2 Raimo A. Ketola,3 and Juha T. Kokkonen3

1Department of Computer Science, Royal Holloway University of London, United Kingdom
2Department of Computer Science, University of Helsinki, Finland
3VTT Processes, Finland
4Department of Computer Science, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, United Kingdom

Copyright © 2005 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


We present a method for determination of the isotopomer distributions of metabolites from the data generated by a tandem mass spectrometer. The method is an improvement over existing method as it is able to deal with overlapping fragments in the spectra. Our experiments indicate that the new method surpasses its predecessors in separating isotopomers from each other. When using the daughter ion scanning (collision induced dissociation) mode, the method was shown to be able to constrain the isotopomer distribution of different amino acids better than two existing methods. In particular, the isotopomer distributions of three amino acids, glycine, alanine and serine, can be fully uncovered with the method. However, due to the imperfect fragmentation of molecules in the tandem mass spectrometer, isotopomer distributions of larger amino acids still cannot be fully uncovered. In tests with isotope-labelled alanine, most accurate results were obtained using multiple reaction monitoring and 15 eV collision energy. The meausured isotopomer frequecies were in the range 99?106% of the theoretical value and the deviation between repetitions was in the range 1?10%.