Ari Rantanen

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We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the(More)
ReMatch is a web-based, user-friendly tool that constructs stoichiometric network models for metabolic flux analysis, integrating user-developed models into a database collected from several comprehensive metabolic data resources, including KEGG, MetaCyc and CheBI. Particularly, ReMatch augments the metabolic reactions of the model with carbon mappings to(More)
BACKGROUND Metabolic fluxes provide invaluable insight on the integrated response of a cell to environmental stimuli or genetic modifications. Current computational methods for estimating the metabolic fluxes from 13C isotopomer measurement data rely either on manual derivation of analytic equations constraining the fluxes or on the numerical solution of a(More)
Metabolic flux estimation—the problem of finding out the rates of reactions in metabolic pathways—is an important problem area in the study of metabolism. The most accurate technique for this task today is the use of isotopic tracer experiments, where a mixture of differently isotope-labeled substrates is fed to a cell culture and the propagation of the(More)
MOTIVATION Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways. However, the development of isotopomer measurement techniques for intermediate metabolites is a demanding task. Careful planning of isotopomer measurements is thus needed to(More)
Recent small-world studies of the global structure of metabolic networks have been based on the shortest-path distance. In this paper, we propose new distance measures that are based on the structure of feasible metabolic pathways between metabolites. We argue that these distances capture the complexity of the underlying biochemical processes more(More)
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(More)
Mass spectrometry is one of the key enabling measurement technologies for systems biology, due to its ability to quantify molecules in small concentrations. Tandem mass spectrometers tackle the main shortcoming of mass spectrometry, the fact that molecules with an equal mass-to-charge ratio are not separated. In tandem mass spectrometer molecules can be(More)
We propose a computational method for reconstructing metabolic networks. The method utilizes optimization techniques and graph traversal algorithms to discover a set of biochemical reactions that is most likely catalyzed by the enzymatic genes of the target organism. Unlike most existing computational methods for metabolic reconstruction, our method(More)
Flux estimation using isotopic tracers is currently the only method that can give quantitative estimated of the activity of metabolic pathways. The success of these methods, however, is intimately dependent on the quality and amount of data on isotopomer distributions of intermediate metabolites. In this paper we present a novel method for discovering sets(More)