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PubMed2001

Fractionation of isotopically labeled peptides in quantitative proteomics.

The goal of quantitative proteomics is to examine the expression levels of all of the proteins in a biological system and recognize those that change as a function of some stimulus. Quantification is now frequently based on derivatization of peptides with isotopically distinguishable labeling agents. This study examines the extent to which isotopic forms of peptides having the same amino acid sequence are resolved by reversed-phase chromatography and assesses the degree to which resolution of these isotopically different forms of a peptide impact quantification. Three derivatizing agents were examined, the do and d3 forms of N-acetoxysuccinimide, the do and d4 forms of succinic anhydride, and the do and d8 forms of the commercial ICAT reagent Peptide mixtures from control and experimental samples were derivatized individually, mixed, subjected to reversed-phase chromatography, and analyzed by ESI-MS. When partial resolution of the isotopic forms of a peptide occurs, the largest error in assessing the true isotope ratio in a sample occurs when sampling at the extremes of a peak. Early in the elution of a peak, the sample will be enriched in the deuterated species, whereas the opposite is true at the tailing edge of a peak. Acetylated peptides showed the lowest degree of separation. Resolution of the deuterated and nondeuterated forms in this case was 0.023. This amounts to slightly over a 1-s difference in their peak maxima and can cause a typical error of +/- 6% at the leading and tailing edges of a peak. In contrast, resolution of the deuterated and nondeuterated forms of the ICAT reagent were calculated to be 0.45. This means that in a peak of 1-min width (W1/2), the peak maxima will vary by approximately 30 s, and measurement errors of -83 and +500% can occur at the leading and tailing edges of a peak. It is concluded that resolution of isotopic forms of a peptide can cause substantial quantification errors in quantitative proteomics.

Angiotensin I↗
PubMed2006

Discovery of novel hippocampal neurogenic agents by using an in vivo stable isotope labeling technique.

Neurogenesis occurs in discrete regions of adult mammalian brain, including the subgranular zone of the hippocampus. Hippocampal neurogenesis is enhanced by different classes of antidepressants, but screening for neurogenic actions of novel antidepressants has been inefficient because of limitations of 5-bromo-2'-deoxyuridine labeling techniques. We describe an efficient in vivo method for measuring hippocampal neurogenesis involving incorporation of the stable isotope, (2)H, into genomic DNA during labeling with (2)H(2)O (heavy water). Male rodents received 8 to 10% (2)H(2)O in drinking water; DNA was isolated from hippocampal progenitor cells or neurons. Label incorporation into progenitor cells of Swiss-Webster mice revealed subpopulation kinetics: 16% divided with t(1/2) of 2.7 weeks; the remainder did not divide over 1 year. Progenitor cell proliferation rates in mice were strain-dependent. Chronic antidepressant treatment for 3 weeks, with (2)H(2)O administered during the final week, increased progenitor cell proliferation across all the strains tested. Fluoxetine treatment increased (2)H incorporation into DNA of gradient-enriched neurons or flow-sorted neuronal nuclei 4 weeks after (2)H(2)O labeling, representing the survival and differentiation of newly divided cells into neurons. By screening 11 approved drugs for effects on progenitor cell proliferation, we detected previously unrecognized, dose-dependent enhancement of hippocampal progenitor cell proliferation by two statins and the anticonvulsant topiramate. We also confirmed stimulatory activity of other anticonvulsants and showed inhibition of progenitor cell proliferation by isotretinoin and prednisolone. In conclusion, stable isotope labeling is an efficient, high-throughput in vivo method for measuring hippocampal progenitor cell proliferation that can be used to screen for novel neurogenic drugs.

Animals↗
PubMed2006

Identification of potential genomic biomarkers of hepatotoxicity caused by reactive metabolites of N-methylformamide: Application of stable isotope labeled compounds in toxicogenomic studies.

The inability to predict if a metabolically bioactivated compound will cause toxicity in later stages of drug development or post-marketing is of serious concern. One approach for improving the predictive success of compound toxicity has been to compare the gene expression profile in preclinical models dosed with novel compounds to a gene expression database generated from compounds with known toxicity. While this guilt-by-association approach can be useful, it is often difficult to elucidate gene expression changes that may be related to the generation of reactive metabolites. In an effort to address this issue, we compared the gene expression profiles obtained from animals treated with a soft-electrophile-producing hepatotoxic compound against corresponding deuterium labeled analogues resistant to metabolic processing. Our aim was to identify a subset of potential biomarker genes for hepatotoxicity caused by soft-electrophile-producing compounds. The current study utilized a known hepatotoxic compound N-methylformamide (NMF) and its two analogues labeled with deuterium at different positions to block metabolic oxidation at the formyl (d(1)) and methyl (d(3)) moieties. Groups of mice were dosed with each compound, and their livers were harvested at different time intervals. RNA was prepared and analyzed on Affymetrix GeneChip arrays. RNA transcripts showing statistically significant changes were identified, and selected changes were confirmed using TaqMan RT-PCR. Serum clinical chemistry and histopathologic evaluations were performed on selected samples as well. The data set generated from the different groups of animals enabled us to determine which gene expression changes were attributed to the bioactivating pathway. We were able to selectively modulate the metabolism of NMF by labeling various positions of the molecule with a stable isotope, allowing us to monitor gene changes specifically due to a particular metabolic pathway. Two groups of genes were identified, which were associated with the metabolism of a certain part of the NMF molecule. The metabolic pathway leading to the production of reactive methyl isocyanate resulted in distinct expression patterns that correlated with histopathologic findings. There was a clear correlation between the expression of certain genes involved in the cell cycle/apoptosis and inflammatory pathways and the presence of reactive metabolite. These genes may serve as potential genomic biomarkers of hepatotoxicity induced by soft-electrophile-producing compounds. However, the robustness of these potential genomic biomarkers will need to be validated using other hepatotoxicants (both soft- and hard-electrophile-producing agents) and compounds known to cause idiosyncratic liver toxicity before being adopted into the drug discovery screening process.

Animals↗
PubMed2002

A site-specific low-enrichment (15)N,(13)C isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acids.

We demonstrate that base and sugar protons within a DNA oligomer can be assigned unambiguously following site-specific 15N,13C isotope incorporation at levels as low as 1% enrichment. This simple and cost-effective methodology is demonstrated on the d(GGGTTCAGG) DNA sequence, which forms a dimeric G-quadruplex containing G.G.G.G tetrads sandwiched between G.(C-A) triads.

Carbon Isotopes↗
PubMed1988

Synthesis of 17O isotope labeled Leu-enkephalin and 17O n.m.r.

Oxygen-17 isotope was introduced into the alpha-carboxyl group of glycine, 1-phenylalanine, 1-leucine and 1-tyrosine by acid catalyzed exchange of 17O from H2O(17) or by acid hydrolysis of respective amino acid methyl esters in H2O(17). Quantitative enrichment of glycine was achieved by acid hydrolysis of amino acetonitrile in H2O(17). For alpha-amino protection in amino acids t-butoxycarbonyl (Boc) group was employed for 17O labeled enkephalin synthesis. Five analogues of Leu-enkephalins (I-V) labeled with 17O at different amino acid residues were synthesized by solid phase method. 17O n.m.r. spectra were measured at 24.4 and 67.8 MHz for Leu-enkephalins 17O labeled at Gly2 and Phe4 positions. A downfield shift was observed for 17O labeled Gly2 Leu-enkephalin upon heating. This shift is indicative of the rupture of intramolecular hydrogen bonds. The preliminary results confirm the hypothesis that an intramolecular hydrogen bond exists between the carbonyl group of Gly2 and NH group of Leu5.

Enkephalin, Leucine↗
PubMed2002

Observation of the glycines in elastin using (13)C and (15)N solid-state NMR spectroscopy and isotopic labeling.

We report the solid-state 13C and 15N NMR of insoluble elastin which has been synthesized in vitro with isotopically enriched glycine. Most of the glycines reside in a domain with good cross-polarization (CP) efficiencies, although surprisingly, a portion resides in an environment that is not detectable using CP. Our data indicate that much of the 13C population resides in regions of significant conformational flexibility. To support these conclusions, we present 13C and 15N cross-polarization with magic-angle-spinning (CPMAS) data in conjunction with "direct-polarization", nonspinning CP, and T1 measurements.

Animals↗
PubMed2000

Protein global fold determination using site-directed spin and isotope labeling.

We describe a simple experimental approach for the rapid determination of protein global folds. This strategy utilizes site-directed spin labeling (SDSL) in combination with isotope enrichment to determine long-range distance restraints between amide protons and the unpaired electron of a nitroxide spin label using the paramagnetic effect on relaxation rates. The precision and accuracy of calculating a protein global fold from only paramagnetic effects have been demonstrated on barnase, a well-characterized protein. Two monocysteine derivatives of barnase, (H102C) and (H102A/Q15C), were 15N enriched, and the paramagnetic nitroxide spin label, MTSSL, attached to the single Cys residue of each. Measurement of amide 1H longitudinal relaxation times, in both the oxidized and reduced states, allowed the determination of the paramagnetic contribution to the relaxation processes. Correlation times were obtained from the frequency dependence of these relaxation processes at 800, 600, and 500 MHz. Distances in the range of 8 to 35 A were calculated from the magnitude of the paramagnetic contribution to the relaxation processes and individual amide 1H correlation times. Distance restraints from the nitroxide spin to amide protons were used as restraints in structure calculations. Using nitroxide to amide 1H distances as long-range restraints and known secondary structure restraints, barnase global folds were calculated having backbone RMSDs <3 A from the crystal structure. This approach makes it possible to rapidly obtain the overall topology of a protein using a limited number of paramagnetic distance restraints.

Amino Acid Substitution↗
PubMed1989

Practical considerations in the use of stable isotope labelled compounds as tracers in clinical studies.

Increasingly widespread usage of stable isotope tracers to aid clinical diagnosis and support basic research has stemmed from both advances in mass spectrometry and the availability of competitively priced labelled compounds. Stable isotopes have been used generally to investigate normal and abnormal metabolic pathways, to estimate energy expenditure and body composition and to quantitate substrate flux and oxidation rates. Despite the fact that the underlying principles relating to the use of stable isotopes for in vivo studies are straightforward, careful consideration must be given to all aspects of human studies. This review highlights some of these, including choice of label and tracer molecule, mode of tracer administration and sampling site, analytical instrumentation, interpretation of data and ethical constraints.

Carbon Isotopes↗
PubMed2005

An automated method for the analysis of stable isotope labeling data in proteomics.

An algorithm is presented for the generation of a reliable peptide component peak table from liquid chromatography-mass spectrometry (LC-MS) and subsequent quantitative analysis of stable isotope coded peptide samples. The method uses chemical noise filtering, charge state fitting, and deisotoping toward improved analysis of complex peptide samples. Overlapping peptide signals in mass spectra were deconvoluted by correlation with modeled peptide isotopic peak profiles. Isotopic peak profiles for peptides were generated in silico from a protein database producing reference model distributions. Doublets of heavy and light labeled peak clusters were identified and compared to provide differential quantification of pairs of stable isotope coded peptides. Algorithms were evaluated using peptides from digests of a single protein and a seven-protein mixture that had been differentially coded with stable isotope labeling agents and mixed in known ratios. The experimental results correlated well with known mixing ratios.

Algorithms↗
PubMed2026

Comprehensive identification of carboxylic acids by using bromine isotope-based chemical isotope labelling and structure-guided molecular network.

Carboxylic acids (CAs) are important contributors to the flavor quality of sauce-flavor Chinese Baijiu, yet their comprehensive analysis remains challenging due to poor ionization efficiency, weak chromatographic retention, and limited annotation capability. Herein, we developed a workflow for the high-coverage discovery and annotation of CAs in Baijiu by coupling chemical isotope labeling-liquid chromatography-mass spectrometry with a structure-guided molecular network strategy (SGMNS). A bromine-containing derivatization reagent, 1-(3-aminopropyl)-3-bromoquinolin-1-ium bromide (APBQ), was designed and synthesized to exploit the natural isotope distribution of bromine and characteristic MS/MS fragmentation behavior. Following APBQ derivatization, the target CAs showed superior chromatographic retention and favorable analytical performance. Based on isotopic peak pairing in MS1 and diagnostic fragment validation in MS2, 372 potential CA derivatives were discovered from pooled Baijiu samples and 355 of them were validated by diagnostic fragments in MS2 spectra. To address the scarcity of derivatized spectral libraries, SGMNS was employed for annotation using a background network constructed from APBQ-labeled candidates derived from the Expanded Chinese Baijiu Compound Database. The developed method was further applied to profile Baijiu samples, revealing pronounced differences in CA composition across the seven fermentation rounds. Notably, rounds 3 to 5 exhibited the largest numbers of differential CAs. This study provided an effective analytical strategy for large-scale CA profiling, offering new insight into the chemical basis of flavor formation during multi-round fermentation of sauce-flavor Baijiu.

Isotope Labeling↗
PubMed2002

Stable isotope labeling pattern of resveratrol and related natural stilbenes.

The stable isotope characterization of resveratrol 1 from Polygonum cuspidatum and of related natural stilbenes 11 and 12 obtained by hydrolysis of the corresponding glucosides 2 and 3 from Rheum is reported. The C(6)-C(2)-C(6) framework of suitably protected derivatives of 1, 2, and 3 has been degraded with ozone to the C(6)-C(1) aldehydes 4, 5, 9, and 10, retaining all hydrogen atoms of the precursors. The natural and synthetic derivatives are characterized and distinguished by natural abundance deuterium nuclear magnetic resonance studies. In the case of anisaldehyde 4 the two series show, as expected, the characteristic difference of the aromatic labeling. The formyl deuterium contents of 4 and 5 from resveratrol are remarkably different, seemingly reflecting the different enrichments existing between positions 3 and 2, respectively, of the phenylpropanoid precursor. The positional delta(18)O values of the extractive materials 1-3 were also determined. In this instance a selective deoxygenation procedure was adopted, leading from 1 to the products 6, 7, and 8. The delta(18)O values of the latter compounds reveal, respectively, those at position 4' and positions 3 and 5 of 1. Similarly, the phenolic products 11 and 12 were converted into 13 and 14. From the delta(18)O values of the single components it is possible to design a detailed map of the oxygen fractionations which characterizes the stilbenes 1-3. In particular, the oxygen present at position 4' of the phenylpropanoid moiety of 1-3 shows delta(18)O values of +11.5, +1.8, and +6.7 per thousand, respectively. Moreover, the phenolic oxygen atom at position 3' of rhapontin 3 shows a value of +11.7 per thousand. The data are compared with those previously obtained on structurally related compounds. These results show the utility of simple chemical degradations in the stable isotope characterization of structurally complex food components.

Deuterium↗