Peptides correlation analysis

The interaction between a solvated peptide and an RPC sorbent in a fully or partially aqueous solvent environment can be discussed in terms of the interplay of weak physical forces. Based on linear free energy considerations, the effects of these forces can, to a first approximation, be linearly summated. Consequently, knowledge of the amino acid sequence of a peptide permits, to a first approximation, the effective hydrophobicity of the peptide to be derived by correlation analysis methods using data derived from other techniques, or... 

A complementary approach to protein identification is based on peptide seqnencing analysis (PSA) by collision-induced dissociation (CID) in MS-MS. Por proteomics studies, the de novo sequencing of MS-MS spectra is too time-consuming. Therefore, algorithms have been developed to either provide antomated MS-MS spectmm interpretation, or perform protein identification by means of a SEQUEST database search [6-7]. In the latter case, the precursor m/z values are matched against a virtual digestion of all the proteins in the database. Sequence ions are predicted for the peptides that match the precnrsor m/z values, and compared with the measured MS-MS data. A correlation score is calculated for each match. 

Accordingly, Kohl et al. reported an in vitro protease assay for two-photon cross-correlation analysis based solely on the fluorescent proteins rsGFP and DsRed [88]. A GFP-peptide-DsRed construct named STEV-ST was purified and subjected to proteolysis separating the fluorophores. With regard to future... 

Kessler, H., Griesinger, C., Zarbock, J., Loosli, H. R. Assignment of carbonyl carbons and sequence analysis in peptides by heteronudear shift correlation via small coupling constants with broad-band decoupling in ft (COLOC)./. Magn. Reson. 1984, 57, 331-336. 

Area analysis of chromatograms is familiar to the chromatographer. The assumption is made that the area of a peak is proportional to the mass of the component present. The spectrophotometric detector is set at about 280 nm to detect the aromatic residues or at 210 to 230 nm to detect the peptide bond. The absorbance at 280 may be influenced by peptide composition, while the absorbance near 220 nm is more closely correlated to mass. 

The m/z values of peptide ions are mathematically derived from the sine wave profile by the performance of a fast Fourier transform operation. Thus, the detection of ions by FTICR is distinct from results from other MS approaches because the peptide ions are detected by their oscillation near the detection plate rather than by collision with a detector. Consequently, masses are resolved only by cyclotron frequency and not in space (sector instruments) or time (TOF analyzers). The magnetic field strength measured in Tesla correlates with the performance properties of FTICR. The instruments are very powerful and provide exquisitely high mass accuracy, mass resolution, and sensitivity—desirable properties in the analysis of complex protein mixtures. FTICR instruments are especially compatible with ESI29 but may also be used with MALDI as an ionization source.30 FTICR requires sophisticated expertise. Nevertheless, this technique is increasingly employed successfully in proteomics studies. 

The mobility of tyrosine in Leu3 enkephalin was examined by Lakowicz and Maliwal/17 ) who used oxygen quenching to measure lifetime-resolved steady-state anisotropies of a series of tyrosine-containing peptides. They measured a phase lifetime of 1.4 ns (30-MHz modulation frequency) without quenching, and they obtained apparent rotational correlation times of 0.18 ns and 0.33 ns, for Tyr1 and the peptide. Their data analysis assumed a simple model in which the decays of the anisotropy due to the overall motion of the peptide and the independent motion of the aromatic residue are single exponentials and these motions are independent of each other. 

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