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 structural information of the MS n product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MS n product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MS n product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive-and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid. Copyright # 2008 John Wiley & Sons, Ltd.Modern systems biological research, such as the study of complete cells or organs, sets heavy requirements to measurement technologies. 1 The measurements on different kinds of biomolecules, sometimes present in very low concentrations, have to be generated in a high-throughput fashion, simultaneously assuring the accuracy of any single measurement. In the midst of these tough requirements, tandem mass spectrometry (MS/MS) has emerged as one of the key technologies in systems biology, finding diverse applications in the 'omics' science, for example in the analysis of proteins (proteomics), metabolite profiles (metabolomics) and metabolic pathway activity (fluxomics). In proteomics studies, MS/MS is routinely applied to identify unknown proteins and quantify their abundances. 2,3 In metabolomics studies, the abundances of tens, even hundreds of metabolites, usually with overlapping masses, are determined. With modern tandem mass spectrometers, such as Fourier transform ion cyclotron resonance (FTICR) and quadrupole-time-of-flight (Q-TOF) instruments, it is not only possible to rapidly discover the accurate masses and intensities of hundreds of compounds with one scan...

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 13 C isotopomer measurement data rely either on manual derivation of analytic equations constraining the fluxes or on the numerical solution of a highly nonlinear system of isotopomer balance equations. In the first approach, analytic equations have to be tediously derived for each organism, substrate or labelling pattern, while in the second approach, the global nature of an optimum solution is difficult to prove and comprehensive measurements of external fluxes to augment the 13 C isotopomer data are typically needed.

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