Stable Isotopes Labeling

The Tools of Proteomics A variety of methods and techniques including two-dimensional gel electrophoresis (2DE), capillary liquid chromatography, stable isotope labeling, and mass spectrometry has been developed for qualitative and quantitative protein... 

Sullivan ER, X Zhang, C Phelps, LY Young (2001) Anaerobic mineralization of stable-isotope-labeled 2-methylnaphthalene. Appl Environ Microbiol 67 4353-4357. 

A phenol-degrading community was examined using phenol followed by analysis of the stable-isotope-labeled RNA by equilibrium density centrifugation, and complemented... 

Characterization of various types of damage to DNA by oxygen-derived species can be achieved by the technique of gas chromatography-mass spectrometry (GC-MS), which may be applied to DNA itself or to DNA-protein complexes such as chromatin (Dizdaroglu, 1991). For GC-MS, the DNA or chromatin is hydrolysed (usually by heating with formic acid) and the products are converted to volatile derivatives, which are separated by gas chromatography and conclusively identified by the structural evidence provided by a mass spectrometer. Stable isotope-labelled bases may be used as internal standards... 

Figure 3.2. Stable isotope labeling for quantifying differential protein expression. Cell populations are grown in either 14N or 15N containing medium. Protein lysates are fractionated and separated by 2D gel electrophoresis. Protein spots are excised, digested with trypsin and the mass of the resulting peptides is determined by mass spectrometry. The presence of 15N results in a shift and creates two peaks for each peptide. The ratio of intensities of the peaks is indicative of the relative expression levels of the proteins. Spot A contains a protein that is expressed at similar levels in both cell pools. Spot B contains a protein that is expressed at higher levels in cell pool 2. Figure adapted from Oda et al. (1999).

Regnier, F. E. Riggs, L. Zhang, R. Xiong, L. Liu, P. Chakraborty A. Seeley E. Sioma, C. Thompson, R. A. Comparative proteomics based on stable isotope labeling and affinity selection. J. Mass. Spectrom. 2002,37,133-145. 

Czerwieniec, G. A. Russell, S. C. Tobias, H. J. Fergenson, D. P. Steele, P Pitesky, M. E. Horn, J. M. Frank, M. Gard, E. E. Lebrilla, C. B. Stable isotope labeling of entire Bacillus atrophaeus spores and vegetative cells using bio-aerosol mass spectrometry. Anal. Chem. 2005, 77,1081-1087. 

Kigawa, T., Yabuki, T., Yoshida, Y. et al. (1999) Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Letters, 442 (1), 15-19. 

The approach recruited to chemical proteomics in Reference [17] is called SILAC (stable isotope labeling with amino acids in cell culture) and is important in comparative proteomics (Figure 1). SILAC works well with cultured mammalian cells, but prokaryotes defeat it by metabolizing the label (usually supplied in lysine and arginine) into other amino acids. For applications beyond cultured eukaryotic cells, the reductive methylation route to differential labeling [18] is among the alternatives [15]-... 

Although use of radio and stable isotope labels involving the trio of covalently-bonded nitrogenous functions in 3 and in 78, provided evidence that isocyano is the precursor of the isothiocyano and formamido groups [30, 81], it remains to be shown that a biosynthetic equivalent of the in vitro chemically-proven fusion process between isocyano and free sulfur (e.g., cf. Introduction) exists in the cells of sponges. In marine biota, various ionic forms of sulfur in a number of oxidation states, as well as organo-polysulfides are known. However, any association with the isonitrile group and a sulfated species has yet to be established. 

Figure 16.6 The solid phase ICAT reagent provides a thiol-reactive iodoacetyl group to capture cysteine peptides, a spacer containing stable isotopic labels, and a photo-cleavable group that can release the captured peptides for mass spec analysis. The VICAT mass tag is a solution phase labeling agent that also has a photo-cleavable site to release isolated peptides from a (strept)avidin affinity resin. This compound adds a fluorescent group to better detect labeled peptides as they are being isolated from a sample.

Guerrero et al. (2006) used this technique along with the quantitative mass spec strategy called SILAC (stable isotope labeling of amino acids in cell culture Ong et al., 2002) to identify the yeast proteins that interact with the 26 S proteasome. 

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D.B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386. 

Elucidation of the physiological role of arachidonic acid 13 and other polyunsaturated fatty acids, particularly the role of all Z-4,7,10,13,16,19-decosahexaenoic acid 14, found in brain, required the corresponding stable-isotope labelled material1011. The deuteriated phosphonium salt 15, the key intermediate used in the synthesis of title compound 16 (equation 8), has been prepared in 19% overall yield12 starting with ethanol-D6 (equation 7). 

The proteomics research of a number of scientists was described in a C E News report of the 2001 Pittcon meeting.10 One group, that of Catherine Fenselau at the University of Maryland, has studied a new method for proteolytic stable isotope labeling to provide quantitative and concurrent comparisons between individual proteins from two entire proteome pools.11 Two lsO atoms are incorporated into the... 

The method development process with the multisorbent plate consists of three steps. In step 1, the sorbent chemistry and the pH for loading, washing, and elution are optimized. In step 2, optimization of the percentage organic for wash and elution and the pH of the buffer needed is carried out. Step 3 is validation the method developed from the results of the previous two steps is tested for linearity, limits of detection, quantitation of recovery, and matrix effects using a stable isotope-labeled analyte as an IS. 

Stable Isotope Labeling in Cell Culture (SILAC)... 

There are two basic aims of chemical derivatization simplification of the fragmentation pattern by either promoting or demoting formation of a chosen ion series, and stable-isotopic labelling for simple assignment of ions to proper ion series (Fig. 6.21). Both methods may provide good results and their advantages and limitations will be discussed. 

Probably, one of the most valuable advances in this field has dealt with the first chemoenzymatic synthesis of the stable isotope-enriched heparin from a uniformly double labelled 13C, 15N /V-acetylheparosan from E. coli K5. Heteronuclear, multidimensional nuclear magnetic resonance spectroscopy was employed to analyze the chemical composition and solution conformation of N-acety 1 hcparosan, the precursors, and heparin. Isotopic enrichment was found to provide well-resolved 13C spectra with the high sensitivity required for conformational studies of these biomolecules. Stable isotope-labelled heparin was indistinguishable from heparin derived from animal tissues and might be employed as a novel tool for studying the interaction of heparin with different receptors.30... 

Pohnert G, Jung V (2003) Intracellular compartmentation in the biosynthesis of caulerpenyne study on intact macroalgae using stable-isotope-labeled precursors. Org Lett 5 5091-5093 Potin P, Bouarab K, Salaun JP, Pohnert G, Kloareg B (2002) Biotic interactions of marine algae. Curr Opin Plant Biol 5 308-317... 

For a quantification an addition of stable isotope-labelled analytes, which exhibit the same chromatographic and ionisation behaviour as their unlabelled analogues present in the sample, and which can be... 

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