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PubMed2001

One approach for doublet deconvolution to improve reliability in spectra analysis for in vivo lead measurement.

Calculation of lead concentration from K-series X-ray fluorescent studies uses a robust normalization technique based on the amplitude or area of the elastic signal. Parameter estimation of the elastic signal can be affected by the overlap of the Kbeta2 line, especially for concentrations greater than 40 ppm where the Kbeta2 amplitude can be greater than 1% of the elastic signal. We tested the combination of estimation by method of least moduli and doublet deconvolution. We found that the estimation of the area of the elastic signal is more robust to changes in the low-energy end of the region of interest with the combined method than with method of least-squares estimation and singlet processing. We recommend use of the combined method for creation of calibration curves at concentrations greater than or equal to 40 ppm.

Bone and Bones↗

PubMedDate not supplied

Determination of the 243 Cm/244 Cm ratio alpha spectrometry and spectral deconvolution in environmental samples exposed to discharges from the nuclear fuel cycle.

The presence of curium nuclides in irradiated nuclear fuel is well known, as is their occurrence in environmental materials exposed to liquid waste discharges from reprocessing plants and to fallout following the Chernobyl accident. Knowledge of the 242 Cm/244 Cm and 243 Cm/244 Cm atom ratios can be a useful tool for characterizing a source-term and assessing the burn-up history of nuclear fuel. Here, a practical technique, based on high-resolution alpha spectrometry and spectral deconvolution, is described by which the 243, 244 Cm multiplet can be resolved at the low activities typical of most environmental samples. The resulting 243 Cm/244 Cm ratio is then used to correct for any interference by 243 Cm in the 242 Cm window. The technique has been applied to the determination of the 243 Cm/244 Cm ratio in samples of seabed sediment collected near the Sellafield outfall, riverine sediment sampled downstream of the Mayak reprocessing plant and soil and lichen from within the Chernobyl exclusion zone. Near Sellafield, the 243 Cm/244 Cm ratio was found to be < 2%, while near Mayak and Chernobyl it was considerably higher, being approximately 6-8%.

Americium↗

PubMed2001

MoWeD, a computer program to rapidly deconvolute low resolution electrospray liquid chromatography/mass spectrometry runs to determine component molecular weights.

A computer program is described that can rapidly process low-resolution electrospray liquid chromatography/mass spectrometry (LC/MS) for peptides and proteins and assign molecular weights for observed components. The program first analyzes individual scans using a deconvolution algorithm similar to that previously described by Zhang and Marshall. Results for the entire run are then sorted by mass and those values found in adjacent scans are grouped together. The list of found components can also be compared to a user defined list of target molecular weight values making it easy to compare the results from different analyses. The program also has the capability to process a rolling average of scans that improves the performance when analyzing high molecular weight components. Other program features facilitate closer examination of selected spectra or regions of the chromatogram to check the MoWeD mass assignments. The utility of the program was demonstrated by the analysis of LC/MS data derived from a complex mixture of proteins derived from a bacterial whole cell lysate that had previously been analyzed manually. The MoWeD analysis was 30 times faster and provided a more comprehensive list of the components present.

Bacillus anthracis↗

PubMed2003

Modeling regional and psychophysiologic interactions in fMRI: the importance of hemodynamic deconvolution.

The analysis of functional magnetic resonance imaging (fMRI) time-series data can provide information not only about task-related activity, but also about the connectivity (functional or effective) among regions and the influences of behavioral or physiologic states on that connectivity. Similar analyses have been performed in other imaging modalities, such as positron emission tomography. However, fMRI is unique because the information about the underlying neuronal activity is filtered or convolved with a hemodynamic response function. Previous studies of regional connectivity in fMRI have overlooked this convolution and have assumed that the observed hemodynamic response approximates the neuronal response. In this article, this assumption is revisited using estimates of underlying neuronal activity. These estimates use a parametric empirical Bayes formulation for hemodynamic deconvolution.

Bayes Theorem↗

PubMed2000

Recent developments in the encoding and deconvolution of combinatorial libraries.

The value of molecular libraries generated by combinatorial methods is largely dependent on the ease and ability to deconvolute or decode the structure of compounds of interest after screening the library. Following the introduction of promising concepts in the early 1990s, there has been considerable progress in the development and refinement of methodologies to address this issue.

Combinatorial Chemistry Techniques↗

PubMed1989

Evidence for radical anion formation during liquid secondary ion mass spectrometry analysis of oligonucleotides and synthetic oligomeric analogues: a deconvolution algorithm for molecular ion region clusters.

It is shown that one-electron reduction is a common process that occurs in negative ion liquid secondary ion mass spectrometry (LSIMS) of oligonucleotides and synthetic oligonucleosides and that this process is in competition with proton loss. Deconvolution of the molecular anion cluster reveals contributions from (M-2H).-, (M-H)-, M.-, and (M + H)-. A model based on these ionic species gives excellent agreement with the experimental data. A correlation between the concentration of species arising via one-electron reduction [M.- and (M + H)-] and the electron affinity of the matrix has been demonstrated. The relative intensity of M.- is mass-dependent; this is rationalized on the basis of base-stacking. Base sequence ion formation is theorized to arise from M.- radical anion among other possible pathways.

Algorithms↗

PubMed2005

Charge ratio analysis method: approach for the deconvolution of electrospray mass spectra.

A new method to interpret electrospray mass spectral data based on calculating the ratio of mass-to-charge (m/z) values of multiply charged ions is described. The mass-to-charge ratios of any two multiply charged ions corresponding to a single compound are unique numbers that enable the charge states for each ion to be unequivocally identified. The multiply charged ions in electrospray mass spectra originate from the addition or abstraction of protons, cations, or anions to and from a compound under analysis. In contrast to existing deconvolution processes, the charge ratio analysis method (CRAM), identifies the charge states of multiply charged ions without any prior knowledge of the nature of the charge-carrying species. In the case of high-resolution electrospray mass spectral data, in which multiply charged ions are resolved to their isotopic components, the CRAM is capable of correlating the isotope peaks of different multiply charged ions that share the same isotopic composition. This relative ratio method is illustrated here for electrospray mass spectral data of lysozyme and oxidized ubiquitin recorded at low- to high-mass resolution on quadrupole ion trap and Fourier transform ion cyclotron mass spectrometers, and theoretical data for the protein calmodulin based upon a reported spectrum recorded on the latter.

Calmodulin↗

PubMed2005

Species-specific isotope dilution analysis and isotope pattern deconvolution for butyltin compounds metabolism investigations.

A methodology for the study of the absorption and metabolism of butyltin compounds in laboratory animals using isotopically enriched species was developed. The method is based on the oral administration of 119Sn-labeled monobutyltin (MBT), 118Sn-labeled dibutyltin (DBT), and 117Sn-labeled tributyltin (TBT) to the animals and the measurement of both the concentration and isotopic composition of these compounds in the different tissues by GC-ICPMS. The degradation of butyltin compounds during their metabolism was computed using least-squares isotope pattern deconvolution, and their concentration was measured by reverse isotope dilution analysis using natural-abundance MBT, DBT, and TBT standards. Male Wistar rats were used as models to evaluate the proposed methodology. Preliminary toxicological results obtained with one rat indicate that TBT is highly absorbed (64.4%), and it is found in all organs with relatively high levels in stomach and intestines. The apparent absorption of DBT was 27.3% and was mainly found in liver, kidney, and intestines. However, a large proportion of the found DBT is formed from the degradation of TBT (approximately 40% of the found DBT in liver is degraded TBT). The apparent absorption of MBT was found to be 12.5%, and the originally administered MBT was mainly recovered in the feces. However, MBT was clearly detected in liver, kidney, stomach, intestines, and urine as degradation products of DBT and TBT. Although a significant variability from rat to rat is expected to be obtained, the analytical variability provided by this methodology is small enough to yield meaningful biological results. The results obtained demonstrate that the developed methodology is able to follow qualitatively, quantitatively, and simultaneously the specific metabolic pathways of different species of a given element.

Animals↗

PubMed2006

Ion/molecule reactions to chemically deconvolute the electrospray ionization mass spectra of synthetic polymers.

A new approach has been developed to analyze synthetic polymers via electrospray ionization mass spectrometry. Ion/molecule reactions, a unique feature of trapping instruments such as quadrupole ion trap mass spectrometers, can be used to chemically deconvolute the molecular mass distribution of polymers from the charge-state distribution generated by electrospray ionization. The reaction involves stripping charge from multiply charged oligomers to reduce the number of charge states. This reduces or eliminates the overlapping of oligomers from adjacent charge states. 15-Crown-5 was used to strip alkali cations (Na+) from several narrow polydisperse poly(ethylene glycol) standards. The charge-state distribution of each oligomer is reduced to primarily one charge state. Individual oligomers can be resolved, and the average molecular mass and polydispersities can be calculated for the polymers examined here. In most cases, the measured number-average molecular mass values are within 10% of the manufacturers' reported values obtained by gel permeation chromatography. The polydispersity was typically underestimated compared to values reported by the suppliers. Mn values were obtained with 0.5% RSD and are independent, over several orders of magnitude, of the polymer and cation concentration. The distributions that were obtained fit quite well to the Gaussian distribution indicating no high- or low-mass discriminations.

Chromatography, Gel↗

PubMed1985

Determination of rotational correlation times from deconvoluted fluorescence anisotropy decay curves. Demonstration with 6,7-dimethyl-8-ribityllumazine and lumazine protein from Photobacterium leiognathi as fluorescent indicators.

The experimental and analytical protocols required for obtaining rotational correlation times of biological macromolecules from fluorescence anisotropy decay measurements are described. As an example, the lumazine protein from Photobacterium leiognathi was used. This stable protein (Mr 21 200) contains the noncovalently bound, natural fluorescent marker 6,7-dimethyl-8-ribityllumazine, which has in the bound state a long fluorescence lifetime (tau = 14 ns). Shortening of the fluorescence lifetime to 2.6 ns at room temperature was achieved by addition of the collisional fluorescence quencher potassium iodide. The shortening of tau had virtually no effect on the rotational correlation time of the lumazine protein (phi = 9.4 ns, 19 degrees C). The ability to measure biexponential anisotropy decay was tested by the addition of Photobacterium luciferase (Mr 80 000), which forms an equilibrium complex with lumazine protein. Under the experimental conditions used (2 degrees C) the biexponential anisotropy decay can best be described with correlation times of 20 and 60 ns, representing the uncomplexed and luciferase-associated lumazine proteins, respectively. The unbound 6,7-dimethyl-8-ribityllumazine itself (tau = 9 ns) was used as a model compound for determining correlation times in the picosecond time range. In the latter case rigorous deconvolution from the excitation profile was required to recover the correlation time, which was shorter (100-200 ps) than the measured laser excitation pulse width (500 ps).

Bacterial Proteins↗

PubMedDate not supplied

One-bead-one-compound library of end-capped dipeptides and deconvolution by microflow NMR.

As part of our program to identify novel small molecules with interesting biological activity, we have designed and synthesized a library of end-capped dipeptides with an emphasis on compound diversity, complexity, and membrane permeability. An approximately 1500-member library was synthesized manually on large polystyrene beads using the mix-and-split method. The final compounds were cleaved into 384-well plates to generate individual stock solutions for input into high-throughput biological screens. Individual compounds were decoded using a combination of mass spectrometry and microflow NMR spectroscopy. In principle, this approach to deconvolution obviates the need for complicated binary encoding-decoding strategies for one-bead-one-compound libraries.

Aminoimidazole Carboxamide↗

PubMed2003

Elimination of 13Calpha splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction.

Homonuclear 13C-13C couplings can significantly reduce the sensitivity and resolution of multidimensional NMR experiments. The most important of these couplings is the 13Calpha-13Cbeta coupling, and several different methods have been developed to eliminate its effect from spectra used for backbone assignment, including short or constant-time evolution periods, selectively labeled amino acids, and multiple-band decoupling sequences. In this communication we show that postacquisition deconvolution of the spectra with a maximum entropy algorithm can be superior to experimental decoupling. The method is very robust, does not introduce shifts of the resonance positions, and simplifies the measurement of the most important NMR experiments for protein backbone assignment.

Carbon Isotopes↗

PubMed1995

Deconvolution of combinatorial libraries for drug discovery: a model system.

Iterative synthesis and screening strategies have recently been used to identify unique active molecules from complex synthetic combinatorial libraries. These techniques have many advantages over traditional screening methods, including the potential to screen large numbers of compounds to identify an active molecule while avoiding analytical separations and structural determination of unknown compounds. It is not clear, however, whether these techniques identify the most active molecular species in the mixtures and, if so, how often. Two key factors which may affect success of the selection process are the presence of many active compounds in the library with a range of activities and the chosen order of unrandomization. The importance of these factors has not been previously studied. Moreover, the impact of experimental errors in determination of subset activities or in randomization during library synthesis is not known. We describe here a model system based on oligonucleotide hybridization that addresses these questions using computer simulations. The results suggested that, within achievable experimental and library synthesis error, iterative deconvolution methods generally find either the best molecule or one with activity very close to the best. The presence of many active compounds in a library influenced the profile of subset activities, but did not preclude selection of a molecule with near optimal activity.

Base Sequence↗

PubMed1996

Deconvolution of combinatorial libraries for drug discovery: experimental comparison of pooling strategies.

An experimental evaluation of several different pooling strategies for combinatorial libraries was conducted using a library of 810 compounds and an enzyme inhibition assay (phospholipase A2). The library contained compounds with varying degrees of activity as well as inactive compounds. The compounds were synthesized in groups of three and pooled together in various formats to realize different pooling strategies. With one exception, all iterative deconvolution strategies and position scanning resulted in identification of the same compound. The results are in good agreement with the predicted outcome from theoretical and computational methods. These data support the tenet that active compounds for pharmaceutically relevant targets can be successfully identified from combinatorial libraries organized in mixtures.

Drug Evaluation, Preclinical↗

PubMed1996

Rediscovering an endothelin antagonist (BQ-123): a self-deconvoluting cyclic pentapeptide library.

A "self-deconvoluting" cyclic pentapeptide library, designed to produce 82,944 head-to-tail-linked peptides in 48 vials, has been prepared. The mixture included amino acids found in a recently optimized endothelin antagonist, BQ-123, originally isolated from microbial sources by Banyu investigators. Using a positional scan approach, the most potent of 12 residues at each of the four variable positions uniquely rediscovered the BQ-123 sequence or cyclo(L-Pro-D-Val-L-Leu-D-Trp-D-Asp). Resynthesis of the four most potent amino acid combinations gave the following values of relative potency: cyclo(L-Pro-D-Val-L-Leu-D-Trp-D-Asp) or BQ-123 = 1.0, cyclo(L-Pro-D-Pro-L-Leu-D-Trp-D-Asp) = 0.0, cyclo(L-Pro-D-Pro-L-Trp-D-Trp-D-Asp) = 0.0, and cyclo(L-Pro-D-Val-L-Trp-D-Trp-D-Asp) = 0.1. This study reflects the first time that the positional scan approach has been applied to cyclic peptide libraries using a known target. Although no analogs more potent than BQ-123 were discovered, our results provide verification of our synthetic methods for preparing head-to-tail cyclic peptide libraries and also lend support to the use of carefully designed sublibraries for the rapid elucidation of potential leads within a relatively constrained set of peptide macrocycles.

Amino Acid Sequence↗

PubMed2005

Metabonomic deconvolution of embedded toxicity: application to thioacetamide hepato- and nephrotoxicity.

We present here the potential of an integrated metabonomic strategy to deconvolute the biofluid metabolic signatures in experimental animals following multiple organ toxicities, using the well-known hepato- and nephrotoxin, thioacetamide. Male Han-Wistar rats were dosed with thioacetamide (150 mg/kg, n = 25), and urine, plasma, liver, and kidney samples were collected postdose for conventional NMR and magic angle spinning (MAS) NMR spectroscopy. These data were correlated with histopathology and plasma clinical chemistry collected at all time points. 1H MAS NMR data from liver and kidney were related to sequential 1H NMR measurements in urine and plasma using pattern recognition methods. One-dimensional 1H NMR spectra were data-reduced and analyzed using principal components analysis (PCA) to show the time-dependent biochemical variations induced by thioacetamide toxicity. From the eigenvector loadings of the PCA, those regions of the 1H NMR spectra, and hence the combinations of endogenous metabolites marking the main phase of the toxic episode, were identified. The thioacetamide-induced biochemical manifestations included a renal and hepatic lipidosis accompanied by hypolipidaemia; increased urinary excretion of taurine and creatine concomitant with elevated creatine in liver, kidney, and plasma; a shift in energy metabolism characterized by depleted liver glucose and glycogen; reduced urinary excretion of tricarboxylic acid cycle intermediates and raised plasma ketone bodies; increased levels of tissue and plasma amino acids leading to amino aciduria verifying necrosis-enhanced protein degradation and renal dysfunction; and elevated hepatic and urinary bile acids indicating secondary damage to the biliary system. This integrated metabonomic approach has been able to identify the tissue of origin for biomarkers present in the metabolic profiles of biofluids, following the onset and progression of a multiorgan pathology, and as such highlights its potential in the evaluation of embedded toxicity in novel drug candidates.

Amino Acids↗

PubMed1996

Determination of tablet coating distribution by deconvolution of uncoated and coated tablet weight distributions.

PURPOSE: The purpose of this research is to obtain the tablet coating distribution from weight distributions of uncoated and coated tablets. METHODS: The method of deconvolution with digital smoothing was used to calculate the distribution of coating applied to a tablet population from separate random measurements of individual uncoated and coated tablets. RESULTS: It was demonstrated that the calculated coating weight distribution agrees well with the measured distribution. The effect of the smoothing factor on the solution is illustrated. CONCLUSIONS: This method can be used during development to facilitate process scale-up/optimization. In routine production, the method can assess the reproducibility and consistency of a coating process.

Chemistry, Pharmaceutical↗

PubMed1995

The application of Fourier deconvolution to reaction time data: a cautionary note.

The Fourier transform method in conjunction with frequency domain smoothing techniques has been suggested as a powerful tool for examining components in a serial, additive reaction time model (P. L. Smith, 1990). Robustness and sensitivity to violations of the assumptions of serial model of this method are evaluated. When an incorrect distribution was used in recovering an unobserved component, results gave no information to show that an incorrect distribution was used, and the results were just as interpretable as those obtained using the correct distribution. These results demonstrate that the assumptions underlying the method cannot be assessed by the result of deconvolution, and the method cannot show that the purported component is actually from the serial combination.

Fourier Analysis↗