Generating functionology
Proceedings of the 2005 ACM symposium on Applied computing
Inferring Peptide Composition from Molecular Formulas
COCOON '09 Proceedings of the 15th Annual International Conference on Computing and Combinatorics
Annotation of LC/ESI-MS mass signals
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
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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.