| Summary: | 博士 === 國立陽明大學 === 生化暨分子生物研究所 === 104 === Protein posttranslational modifications (PTMs) affect the physiochemical properties of modified proteins and have important roles in regulation of numerous biological functions. There have been many different approaches developed for PTM analysis. However, due to the diversity, heterogeneity and low abundance of PTMs, it is difficult to comprehensively study PTMs in one analysis. It has been observed that a chemical property is common to many different types of protein modifications, namely a modified peptide and its non-modified counterpart usually share a similar elution property, when analyzed with reverse phase liquid chromatography. In this study, we report the development of an informatics approach for screening multiple types of protein PTMs based on the close elution property. Our approach features the generation of segmental average mass spectra (saMS) for locating a PTM-bearing peptide in the liquid chromatography-mass spectrometric (LC-MS) data. In order to facilitate the data processing, we have implemented a set of in-house computer programs to the saMS analysis. This saMS approach had been used to identify modified peptides of ROCK2 proteins, and multiple types of PTMs, such as phosphorylation and hexosylation, were discovered. Our method had also been employed to characterize PTMs in ribosomal proteins; various types of modifications were found in different ribosomal protein subunits, including phosphorylation, methylation, acetylation and nitration. Most of these modifications were newly identified, particularly those that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Our discovery of many novel modification sites showcases the prowess of this approach in proteomic PTM studies.
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