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A gas chromatographic/mass spectrometric method for the simultaneous quantitation of 5,5-diphenylhydantoin (phenytoin), its para-hydroxylated metabolite and their stable isotope labelled analogs.

A stable isotope dilution method for the quantitation by GC-MS of 5,5-diphenylhydantoin, its major metabolite (5-(4-hydroxyphenyl)-5-phenylhydantoin), and, simultaneously, their stable isotope labelled analogs (5,5-diphenyl-2-(13)C-1,3-(15)N2-hydantoin and 5-(4-hydroxyphenyl)-5-phenyl-2-(13)C-1,3-(15)N2-hydantoin) is discussed and evaluated. 5,5-di-(pentadeuterophenyl)hydantoin and 5-(4-hydroxy-3,5-dideuterophenyl)-5-phenyl-2-(13)C-1,3(15)N2-hydantoin are used as internal standards. The chemical work-up procedure of serum (1.0 ml) and urine (0.5 ml) involves acid hydrolysis, extraction at pH 7.4 and permethylation of drug and metabolite analogs by extractive methylation. The mass spectrometric technique consists of repetitive scanning over the molecular ion region of the permethylated derivatives of the phenytoin and para-hydroxy metabolite analogs as they elute from the gas chromatograph. Molecular ion abundances are measured. Reproducibility, selectivity and linearity of the method are discussed in the light of the planned applications.

Carbon Radioisotopes↗

Synthesis of isotopically labeled saturated fatty acids.

An approach to the synthesis of isotopically labeled saturated fatty acids is outlined which is based on the copper-catalyzed coupling of an omega-bromo acid with an isotopically labeled Grignard reagent. The method provides high yields of pure products and offers considerable flexibility in the type of isotopically enriched compound that can be prepared.-DasGupta, S. K., D. M. Rice, and R. G. Griffin. Synthesis of isotopically labeled saturated fatty acids.

Deuterium↗

Investigation of intramolecular proton migration in a series of model, metal-cationized tripeptides using in situ generation of an isotope label.

In this study we used an isotope label, generated in situ, to investigate intramolecular proton migration or scrambling during formation of [b(2)+17+Li](+) products by collision-induced dissociation (CID) of Li(+)-cationized tripeptides. To generate the isotope label, we used a McLafferty-type rearrangement of N-terminally acetylated, C-terminal peptide tert-butyl esters in which all amide positions were exchanged with deuterium. Using a set of small, model peptides, we show that intramolecular proton scrambling occurs during CID, particularly amongst adjacent sites along a peptide backbone, on the time scales employed for low-energy collisional activation in an ion-trap mass spectrometer.

Cations↗

Isotope-labeled immunoassays without radiation waste.

The practice of immunoassay has experienced a widespread transition from radioisotopic labeling to nonisotopic labeling over the last two decades. Radioisotope labels have drawbacks that hamper their applications: (i) perceived radiation hazards of reagents, (ii) regulatory requirements and disposal problems of working with radioactive materials, and (iii) short shelf-life of the labeled reagents. The advantage of isotopic labeling is the incorporation into analytes without altering structure or reactivity, as is often the case with ELISA or fluorescent detection systems. We developed a format for isotope label immunoassay with the long-life isotope (14)C as the label and accelerator mass spectrometer (AMS) as the detection system. AMS quantifies attomole levels of several isotopes, including (14)C. With this exquisite sensitivity, the sensitivity of an immunoassay is limited by the K(d) of the antibody and not the detection system. The detection limit of the assays for atrazine and 2,3,7,8-tetrachlorodibenzo-p-dioxin was 2.0 x 10(-10) M and 2.0 x 10(-11) M, respectively, approximately an order of magnitude below the standard enzyme immunoassay. Notably, <1 dpm (0.45 pCi) of (14)C-labeled compound was used in each assay, which is well below the limit of disposal (50 nCi per g) as nonradioactive waste. Thus, endogenous reporter ligands quantified by AMS provide the advantages of an RIA without the associated problems of radioactive waste.

Animals↗

A practical method for uniform isotopic labeling of recombinant proteins in mammalian cells.

A method to obtain uniformly isotopically labeled (15N and 15N/13C) protein from mammalian cells is described. The method involves preparation of isotopically labeled media consisting of amino acids isolated from bacterial and algal extracts supplemented with cysteine and enzymatically synthesized glutamine. The approach is demonstrated by producing 15N-labeled and 15N/13C-labeled urokinase from Sp2/0 cells and successfully growing Chinese hamster ovary (CHO) cells on the labeled media. Thus, using the procedures described, isotopically labeled proteins that have been expressed in mammalian cells can be prepared, allowing them to be studied by heteronuclear multidimensional NMR techniques.

Amino Acids↗

Amino acid residue specific stable isotope labeling for quantitative proteomics.

Various stable isotope labeling (SIL) techniques have recently emerged to improve the efficiency and accuracy of protein quantitation by mass spectrometry (MS). We have developed a mass-tagging strategy to incorporate stable isotope tagged amino acids into cellular proteins in a residue-specific manner during cell growth. In this study, we further extend this residue-specific SIL approach to the accurate quantitation of protein abundances in different cell populations. For proteins whose expression levels are the same in cells grown in the normal and labeled media, the relative areas of the normal (light) and labeled (heavy) isotopic peaks are linearly correlated with the cells mixing ratios. This approach was first used to determine the effect of the zinc-responsive transcription factor Zap1 on the yeast proteome. Ten protein spots from a PAGE gel were chosen randomly and their differential protein expression levels in wild-type and zap1delta cells were readily determined by the isotopic ratio. Methionine synthase (Met6) was identified to be up-regulated more than four times in the zap1delta mutant strain whereas the expression level of other nine proteins remained unchanged. Further, we applied this strategy to study the cellular response to radiation in human skin fibroblast cells. Analyzing one protein band randomly selected from SDS-PAGE, the expression level of a novel protein was found to increase two-fold in response to radiation whereas the expression level of a control protein remained unchanged. This strategy is generally applicable using any particular type of amino acid as the labeling precursors for accurate quantitation of protein relative abundances.

Amino Acid Sequence↗

Automated comparative proteomics based on multiplex tandem mass spectrometry and stable isotope labeling.

Comparative proteomic approaches using isotopic labeling and MS have become increasingly popular. Conventionally quantification is based on MS or extracted ion chromatogram (XIC) signals of differentially labeled peptides. However, in these MS-based experiments, the accuracy and dynamic range of quantification are limited by the high noise levels of MS/XIC data. Here we report a quantitative strategy based on multiplex (derived from multiple precursor ions) MS/MS data. One set of proteins was metabolically labeled with [13C6]lysine and [15N4]arginine; the other set was unlabeled. For peptide analysis after tryptic digestion of the labeled proteins, a wide precursor window was used to include both the light and heavy versions of each peptide for fragmentation. The multiplex MS/MS data were used for both protein identification and quantification. The use of the wide precursor window increased sensitivity, and the y ion pairs in the multiplex MS/MS spectra from peptides containing labeled and unlabeled lysine or arginine offered more information for, and thus the potential for improving, protein identification. Protein ratios were obtained by comparing intensities of y ions derived from the light and heavy peptides. Our results indicated that this method offers several advantages over the conventional XIC-based approach, including increased sensitivity for protein identification and more accurate quantification with more than a 10-fold increase in dynamic range. In addition, the quantification calculation process was fast, fully automated, and independent of instrument and data type. This method was further validated by quantitative analysis of signaling proteins in the EphB2 pathway in NG108 cells.

Amino Acid Sequence↗

Isotopic labeling of recombinant proteins expressed in the protozoan host Leishmania tarentolae.

Isotope labeling of recombinant proteins is a prerequisite for application of nuclear magnetic resonance spectroscopy (NMR) for the characterization of the three-dimensional structures and dynamics of proteins. Overexpression of isotopically labeled proteins in bacterial or yeast host organisms has several drawbacks. In this work, we tested whether the recently described eukaryotic protein expression system based on the protozoa Leishmania tarentolae could be used for production of amino acid specific (15)N-labeled recombinant proteins. Using synthetic growth medium we were able to express in L. tarentolae and purify to homogeneity (15)N-valine labeled Enchanced Green Fluorescent Protein (EGFP) with the final yield of 5.7 mg/liter of suspension culture. NMR study of isolated EGFP illustrated the success of the labeling procedure allowing identification of all 18 valine residues of the protein in the HSQC spectrum. Our results demonstrate the suitability of the L. tarentolae expression system for production of isotopically labeled proteins.

Animals↗

In vivo uniform (15)N-isotope labelling of plants: using the greenhouse for structural proteomics.

Isotope labelling of proteins is important for progress in the field of structural proteomics. It enables the utilisation of the power of nuclear magnetic resonance spectroscopy (NMR) for the characterisation of the three-dimensional structures and corresponding dynamical features of proteins. The usual approach to obtain isotopically labelled protein molecules is by expressing the corresponding gene in bacterial or yeast host organisms, which grow on isotope-enriched media. This method has several drawbacks. Here, we demonstrate that it is possible to fully label a plant with (15)N-isotopes. The advantage of in vivo labelling of higher organisms is that all constituting proteins are labelled and become available as functional, post-translationally modified, correctly folded proteins. A hydroponics set-up was used to create the first example of a uniformly (15)N-labelled (> 98%) plant species, the potato plant (Solanum tuberosum L., cv. Elkana). Two plants were grown at low costs using potassium-[(15)N]-nitrate as the sole nitrogen source. At harvest time, a total of 3.6 kg of potato tubers and 1.6 kg of foliage, stolons and roots were collected, all of which were fully (15)N-labelled. Gram quantities of soluble (15)N-labelled proteins (composed mainly of the glycoprotein patatin and Kunitz-type protease inhibitors) were isolated from the tubers. NMR results on the complete proteome of potato sap and on an isolated protease inhibitor illustrate the success of the labelling procedure. The presented method of isotope labelling is easily modified to label other plants. Its envisioned impact in the field of structural proteomics of plants is discussed.

Carbon Isotopes↗

[Use of DNA-methylases as reagents for the production of isotopically labeled DNAs].

The method of incorporation of an isotopic label into DNA by means of DNA-methyltransferases (DNA-methylases) is proposed. DNA was no degraded and retained its biological activity in the DNA-methylase reaction. The specific activity of labelled DNA preparations can be increased, using the mixtures of different DNA-methylases in the enzymatic reaction. An isotopic label was incorporated into DNA, using DNA methylases M. .EcoRII, M.Eco dam and M.EcoMRE600 dcmI. An average activity of 1 microgram of labelled DNA preparations produced by S-adenosylmethionine (methyl-3H) with specific activity of 15 CU/mmol mas about 1 x 10(5) cpm.

DNA↗

Heavy isotope labeling study of the turnover of forskolin-stimulated adenylate cyclase in BC3H1 cell line.

We have used the method of heavy isotope labeling to study the metabolic turnover of adenylate cyclase in a nonfusing muscle cell line, the BC3H1 cells. These cells contains an adenylate cyclase coupled to beta-adrenergic receptors and highly stimulated by forskolin, a potent activator of the enzyme. After transfer of the cells from normal medium to heavy medium (a medium containing heavy labeled amino acids, 2H, 13C, 15N), heavy isotope-labeled adenylate cyclase molecules progressively replace pre-existing light molecules. In sucrose gradient differential sedimentation, after a 5-day switch in heavy medium, the enzyme exhibited a higher mass (s = 8.40 +/- 0.03 S, n = 13) compared to the control enzyme (s = 7.40 +/- 0.04 S, n = 36). Indeed, the increase in the sedimentation coefficient of the heavy molecules was due to the synthesis of new molecules of adenylate cyclase labeled with heavy isotope amino acids since in the presence of cycloheximide, an inhibitor of protein synthesis, no change in the sedimentation pattern of the forskolin-stimulated adenylate cyclase occurred. After incorporation of heavy isotope amino acids in the adenylate cyclase molecules, the kinetics parameters of the enzyme (i.e. Km for ATP and EC50 for Mn2+ or Mg2+) did not change. However, adenylate cyclase from cells incubated with heavy medium exhibits an activity about 2-fold lower than control (cells in light medium). After switching the cells to the heavy medium, the decrease of the activity of the enzyme occurred during the first 24 h and thereafter remained at a steady state for at least 4 days. In contrast, 24 h after the switch, the sedimentation coefficient of forskolin-stimulated adenylate cyclase was progressively shifted to a higher value indicating that the heavy isotope-labeled enzyme replaced the pre-existing light form of the molecule. These observations show that the rapid decrease in adenylate cyclase activity and the synthesis of heavy adenylate cyclase molecules are two separate events. The relative amounts of heavy and light components of forskolin-stimulated adenylate cyclase obtained in sucrose gradient differential sedimentation were determined as a function of time beginning 24 h after the transfer into the heavy medium. The decrease of the pre-existing light form could be represented by simple first order kinetics with a half-time of 40 h. This result suggests that the metabolic renewal of forskolin-stimulated adenylate cyclase is comparable to that of most plasma membrane proteins.

Adenylyl Cyclases↗

A multiple mass spectral line method for determining positional specific activities in stable isotope-labeled amino acids.

A method for determining the position and enrichment of isotope labels in amino acids using gas chromatography/mass spectrometry is described. [alpha-15N]- and [epsilon-15N]lysine, [1-13C]- and [15N]alanine and -leucine, and [1-13C]-, [2-13C]-, [3-13C]-, and [4-13C]aspartic acid were investigated. Standards for each isotope label were prepared and analyzed under scan conditions, and line pairs characteristic for the label were identified. The standards were reanalyzed under selective ion monitoring conditions to verify the behavior of the line pairs. Mixtures of amino acids containing different isotope labels or the same label in different positions were prepared and analyzed under selective ion monitoring conditions. Enrichments were determined with high precision and relative errors ranging from 0.14 to 36%.

Amino Acids↗

Use of stable isotopically labeled tracers for studies of metabolic kinetics: an overview.

Stable isotopically labeled tracers offer a reliable and safe alternative to the use of radioactive tracers for studies of metabolic kinetics. This overview examines some of the principles and technical issues regarding mass spectrometry instrumentation, and reviews some of the approaches used in the application of stable isotopically labeled tracers to studies of protein, lipid, and carbohydrate metabolic kinetics.

Elements↗

Use of stable isotopically labeled benzene to evaluate environmental exposures.

The use of stable, isotopically labeled compounds in controlled exposure experiments at environmentally relevant levels allows for the distinguishing of urinary metabolites associated with known exposure from background levels generally present in the urine. Exposures of volunteers to (13)C-benzene for 2 h at 40+/-10 p.p.b. were conducted after obtaining informed consent, and urinary phenol, catechol, hydroquinone and trans,trans- muconic acid were measured. Each isotopically labeled urinary metabolite was determined in the presence of significantly higher concentrations of the unlabeled metabolite. Following exposure, free and acid hydrolyzed phenol, acid hydrolyzed catechol and hydroquinone, and free trans,trans-muconic acid were determined by GC/MS. The percentage of trans,trans-muconic acid excreted was higher than reported following exposure at occupational levels. The use of isotopically labeled compounds has the potential to investigate the metabolism of common environmental contaminants for validation of toxicokinetic models and improve risk extrapolation from high concentration occupational exposures and animal studies to environmentally relevant pollutant levels.

Adult↗

Enzyme-assisted preparation of isotope-labeled 1-deoxy-d-xylulose 5-phosphate.

Recombinant 1-deoxy-D-xylulose 5-phosphate synthase of Bacillus subtilis was used for the preparation of isotope-labeled 1-deoxy-D-xylulose 5-phosphate using isotope-labeled glucose and/or isotope-labeled pyruvate as starting materials. The simple one-pot methods described afford almost every conceivable isotopomer of 1-deoxy-D-xylulose 5-phosphate carrying (13)C or (14)C from commercially available precursors with an overall yield around 50%.

Bacillus subtilis↗

Synthesis of isotopically labelled retinal. Structural and functional studies at the atomic level of the chromophore in visual pigments.

OBJECTIVE: To describe the strategy followed in studying the structure and function of the chromophore in visual pigments at the atomic level. METHODS: A three-step strategy was followed. First, 11-cis retinal with high enrichment (99% 13C or 99% 2H) at pre-determined positions or combinations of positions was synthesized. Second, the rhodopsins with isotope label in the chromophore were prepared combining opsin with the isotopically labelled 11-cis retinal. Third, these systems were studied with isotope-sensitive physical techniques. CONCLUSIONS: Isotope labelling together with isotope-sensitive spectroscopy is a highly promising method for obtaining information at the atomic level of biologically active systems. Strategies based on specific stable isotope labelling are likely to be applicable to many research areas.

Carbon Isotopes↗

A method for automatically interpreting mass spectra of 18O-labeled isotopic clusters.

16O/18O labeling is one differential proteomics technology among many that promises diagnostic and prognostic biomarkers of disease. Although the incorporation of 18O in the C-terminal carboxyl group during endoproteinase digestion in the presence of H2 18O makes the process of labeling facile, the ease and effectiveness of label incorporation have in some regards been outweighed by the difficulties in interpreting the resulting spectra. Complex isotope patterns result from the composition of unlabeled (18O(0)), singly labeled (18O(1)), and doubly labeled species (18O(2)) as well as contributions from the naturally occurring isotopes (e.g. 13C and 15N). Moreover because labeling is enzymatic, the number of 18O atoms incorporated can vary from peptide to peptide. Finally it is difficult to distinguish highly up-regulated from highly down-regulated or C-terminal peptides. We have developed an algorithm entitled regression analysis applied to mass spectrometry (RAAMS) that automatically, rapidly, and confidently interprets spectra of 18O-labeled peptides without requiring chemical composition information derived from product ion spectra. The algorithm is able to measure the effective 18O incorporation rate due to variable enzyme substrate specificity of the pseudosubstrate during the isotope exchange reaction and corrects for the 18O(0) abundance that remains in the labeled sample when using a two-step digestion/labeling procedure. We have also incorporated a method for distinguishing pure 18O(0) from pure 18O(2) peptides utilizing impure H2 18O. The algorithm operates on centroided peak lists and is therefore very fast: nine chromatograms of, on average, 1,168 spectra and containing, on average, 6,761 isotopic clusters were interpreted in, on average, 45 s per chromatogram. RAAMS is fast enough (average, 38 ms/spectrum) to allow the possibility of performing information-dependent MS/MS on a chromatographic time scale on species exceeding predetermined ratio thresholds. We describe in detail the operation of the algorithm and demonstrate its use on datasets with known and unknown ratios.

Algorithms↗

Semiparametric modeling of labeled-cell kinetics, with application to isotope labeling of erythrocytes.

We propose a stochastic model for the kinetics of cells that have been tagged with a chemical label. The proposed model consists of two components: a parametrically specified distribution for the time to incorporation of the label into the cells and a nonparametric survival function reflecting the survival time of the label-cell combination. The target quantity of this modeling approach is the fraction of labeled cells among all cells, viewed as a function of time. Longitudinal measurements of this labeled-cell fraction are available from a recent experiment with folate-labeled red blood cells. The proposed semiparametric model is fitted to these data and some of the implications are explored. The proposed method also includes bootstrap-based inference.

Carbon Radioisotopes↗