title: Computing positional isotopomer distributions from tandem mass spectrometric data.
abstract: The isotopomer distributions of metabolites are invaluable pieces of information in the computation of the flux distribution in a metabolic network. We describe the use of tandem mass spectrometry with the daughter ion scanning technique in the discovery of positional isotopomer distributions (PID). This technique increases the possibilities of mass spectrometry since given the same fragment ions, it uncovers more information than the full scanning mode. The mathematics of the new technique is slightly more complicated than the techniques needed by full scanning mode methods. Our experiments, however, show that in practice the inadequacy of the fragmentation of amino acids in the tandem mass spectrometer does not allow uncovering the PID exactly even if the daughter ion scanning is used. The computational techniques have been implemented in a MATLAB application called PIDC (Positional Isotopomer Distribution Calculator).
authors.affiliation: Department of Computer Science, FIN-00014 University of Helsinki, Finland. ari.rantanen@cs.helsinki.fi
authors.forename: Ari
authors.initials: A
authors.lastname: Rantanen
authors.forename: Juho
authors.initials: J
authors.lastname: Rousu
authors.forename: Juha T
authors.initials: JT
authors.lastname: Kokkonen
authors.forename: Virpi
authors.initials: V
authors.lastname: Tarkiainen
authors.forename: Raimo A
authors.initials: RA
authors.lastname: Ketola
mesh_terms: D000409:Alanine / Q000032:analysis / Q000737:chemistry; D000465:Algorithms; D000596:Amino Acids / Q000032:analysis / Q000737:chemistry; D002247:Carbon Isotopes / Q000032:analysis* / Q000737:chemistry*; D002853:Chromatography, Liquid / Q000379:methods; D007536:Isomerism; D007553:Isotope Labeling / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods
chemical_list: D000596:Amino Acids; D002247:Carbon Isotopes; D000409:Alanine