Computing positional isotopomer distributions from tandem mass spectrometric data

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 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 methods. Our experiments, however, show that in the practice the inadequancy 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 appication called PIDC (Positional Isotopomer Distribution Calculator).