Mass spectrometry protein modification detection

The second method also relies on site-specific chemical modification ofphosphoproteins (Oda et al., 2001). It involves the chemical replacement of phosphates on serine and threonine residues with a biotin affinity tag (Fig. 2.7B). The replacement reaction takes advantage of the fact that the phosphate moiety on phosphoserine and phosphothreonine undergoes -elimination under alkaline conditions to form a group that reacts with nucleophiles such as ethanedithiol. The resulting free sulfydryls can then be coupled to biotin to create the affinity tag (Oda et al., 2001). The biotin tag is used to purify the proteins subsequent to proteolytic digestion. The biotinylated peptides are isolated by an additional affinity purification step and are then analyzed by mass spectrometry (Oda et al., 2001). This method was also tested with phosphorylated (Teasein and shown to efficiently enrich phosphopeptides. In addition, the method was used on a crude protein lysate from yeast and phosphorylated ovalbumin was detected. Thus, as with the method of Zhou et al. (2001), additional fractionation steps will be required to detect low abundance phosphoproteins. 

Meng, F., Forbes, A.J., Miller, L.M., Kelleher, N.L. (2005). Detection and localization of protein modifications by highresolutiontandemmass spectrometry. Mass Spectrom. Rev. 24,126-134. 

Mass spectrometry (MS) is widely used to ascertain the purity, total mass of the protein produced, and detect any covalent modifications (Cohen and Chait, 2001). Both electrospray ionization (ESI) and MALDI may be used although for intact proteins ESI has the advantage of being accurate to 1 Da. Using the simple protocol described in Protocol 2.11, the MS of whole protein samples can be readily automated without the need for sample preparation. This method has proved successful for the... 

Carr SA, Annan RS, Huddleston MJ. Mapping posttranslational modifications of proteins by MS-based selective detection Application to phosphoproteomics. In Burlingame AL, ed.. Mass Spectrometry Modified Proteins and Glycoconjugates, Vol. 405, New York Academic Press, 2005, 82-115. 

Mass spectrometry provides a wealth of information for proteomics research, enzymology, and protein chemistry in general. The techniques require only miniscule amounts of sample, so they can be readily applied to the small amounts of protein that can be extracted from a two-dimensional electrophoretic gel. The accurately measured molecular mass of a protein is one of the critical parameters in its identification. Once the mass of a protein is accurately known, mass spectrometry is a convenient and accurate method for detecting changes in mass due to the presence of bound cofactors, bound metal ions, covalent modifications, and so on. 

Pentosidine is determined by HPLC with spectrofluorimetric detection (excitation and emission wavelengths of 335 and 385 nm, respectively) (S14), although immunochemical and ELISA assays for determination of various protein oxidative modification products have become increasingly popular (08). Protein-aldehyde adducts can be estimated using adduct-specific antibodies (U2, Wl). Another approach requires stabilization of adducts, producing derivatives resistant to conditions used in protein acid hydrolysis and quantification of hydrolysis products by gas chromatography-mass spectrometry (R7). 

MALDI quadrupole ion trap mass spectrometry has also been used to localize and identify the post-translational modifications on the Sindai virus [18]. The polymerase associated protein (P protein) from this virus is reported in the literature to be highly phosphorylated. In vitro studies have detected phosphorylation in different regions of the protein, while a single phosphorylation site was found in the in vivo studies. Mass spectral data, along with computer-aided analysis, enabled the identification and localization of two phosphorylation sites. 

The dioxygen reduction site of the key respiratory enzyme, cytochrome c oxidase [E.C. 1.9.3.1], is a bimetallic catalytic center comprised of a heme iron adjacent to a Type 2 mononuclear copper center (see Cytochrome Oxidase). The recent solution of the X-ray crystal structure of this enzyme revealed an entirely unanticipated covalent modification of the protein structure, a cross-link between a histidine and tyrosine side chain (23) within the active site (Figure 2)." This extraordinary posttranslational modification has been confirmed by peptide mapping and mass spectrometry, and has been detected as a conserved element in cytochrome c oxidases isolated from organisms ranging from bacteria to cows. The role of the cross-linked structure in the function of cytochrome c oxidase is still controversial." " ... 

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