Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites) that appear in a person’s biofluids, which means such diseases can often be readily detected from a person’s “metabolic profile"—i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR) spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person’s metabolic profile. Given a 1D 1 H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid), BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the “signatures” of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF), defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error), in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively—with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. BAYESIL is accessible at http://www.bayesil.ca.

The NMR spectra of naturally occurring iron-sulfur proteins have been studied for some 15 years by now1"4 and yet are not fully understood because there is disagreement between the reported spectra and those expected on a theoretical basis. We have investigated the NMR spectra of a reduced 2Fe-2S protein over a quite extended spectral width and detected some more signals that may provide the key for the assignment of the NMR spectra of every kind of ironsulfur cluster. Six to eight signals had been detected1•4"10 *in several reduced 2Fe-2S ferredoxins (one iron(III) and one iron(II)) in the range from 45 ppm downfield to 5 ppm upfield from DSS, four of them showing an anti-Curie type temperature dependence and the remaining a Curie type temperature dependence. The first idea was to assign the isotropically shifted signals to /3-CH2's of the four bound cysteines.1 7•6 Subsequently, the four signals showing anti-Curie behavior were assigned to the ß-CH2's of the cysteines coordinated to the iron(II) center.4•5

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Oxidized ferredoxin from Clostridium acidi urici, containing two [Fe4S4I2+ clusters, has been investigated through 1H NOESY and TOCSY spectroscopies. The protons of coordinated cysteines have been identified and assigned to each cluster with use of a procedure based on the assignment of two spatially close @CH2 pairs and on the shift ratios of each PCH2 proton in oxidized, half-reduced, and reduced forms; each cysteine proton has been then sequence-specifically and stereospecifically assigned by looking for dipolar connectivities with amino acid residues in the vicinity of the cluster. By comparing the present data with the available spectra of the analogous protein from Clostridium pasteurianum, the sequence-specific and stereospecific assignments of cysteine protons have been obtained also for the latter protein. The natural abundance 13C signals of the cysteine protons have been also sequencespecifically assigned. By taking advantage of the X-ray structure of a similar protein, the lH and I3C hyperfine shifts have been related to the dihedral angle between the iron-sulfur-0-carbon plane and the sulfur-fl-carbon-@-proton or sulfur-/3-carbon-a-carbon planes. A parametric equation is proposed. The spin delocalization mechanism has been found to be largely dependent on unpaired spin density on the pz orbital of the sulfur atom. Through EXSY spectroscopy, the proton signals of the [Fe&]+ clusters in the reduced protein have been assigned. Their temperature dependence is compared with that of the [Fe&I3+ clusters present in oxidized HiPIPs and discussed in terms of the Heisenberg model for the magnetic exchange coupling within the clusters.