フラグメンテーションと同位体解析

抄録

Protein profiling of biological or clinical samples with MS has become a powerful tool, which could lead to new insights into biology or diagnoses of diseases. However, it still has, at least, two issues to be improved, i.e. poor interpretation on isotopic ion distributions and fragmentations in MS, and diversity on fragmentation efficiency, which greatly depends on the instrumentation of MS. Here, we present the applications of the recently developed software, on the first issue, for interpretation of MS or MS/MS spectra.
Various stable-isotope labeling techniques have been reported for use in quantitative comparisons between paired samples in proteomic expression analyses by MS. However, interpretation of such mass spectra is far from being fully automated, mainly due to the difficulty of analyzing complex patterns resulting from the overlap of multiple peaks arising from the assortment of natural isotopes. In order to facilitate the interpretation of a complex mass spectrum of such a mixture, we developed a software application, "Isotopica" (http://coco.protein.osaka-u.ac.jp/Isotopica), that enables the automatic matching of theoretical isotope envelopes to multiple ion peaks in a spectrum, and report here some recent applications for quantitative proteomics.
Relative intensities of fragment ions observed in a MS/MS spectrum reflect the propensities of chemical bonds to be cleaved in gaseous phase. In case of peptides, the side-chain structures of amino acid residues could influence the fragility of a peptide backbone upon CID. Thus, the fragmentation probabilities for a, b, c, x, y", and z-series ions were estimated as a function of amino acid residues at the cleavage sites, based on 22,392 MS/MS spectra obtained by a MALDI-TOF/TOF instrument, and applied for constructing a model of fragmentation pattern. The model has been in good correlation with actual spectra, and could be successfully used for improving the results of peptide identification.