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Proteins are the carriers of biological structure and function, which are involved in almost all the physiological processes in organisms. The qualitative and quantitative analysis of proteins can not only help us understand the mechanisms of life activities, but also screen for the proteins with abnormal expression compared to healthy controls as biomarkers of diseases as well as environmental exposure to harmful substances, thus facilitating to unravel the mechanisms of disease generation and development. Tandem mass spectrometry (MS/MS) is currently the main tool for high-throughput proteomics analysis. It can characterize the proteins by determining the molecular mass of digestion products, locating modification sites, and obtaining sequence information. However, acidic amino acid residues often have a significant impact on the cleavage process of peptides, limiting the performance of MS/MS. For example, for the phosphopeptides containing abundance of negatively charged carboxyl and phosphoryl groups, their ionization is not efficient in the positive mode, and neutral loss is easy to occur during the cleavage process, resulting in a low coverage of product ions in the MS/MS spectra. In this paper, the carboxyl groups from the R group of aspartic acid and glutamic acid as well as the C-terminus of peptide were neutralized using dimethylamine derivatization under mild condition. Accordingly, the fragmentation features of peptides with altered charge properties were studied in collision-induced dissociation (CID) mode. Further, the peptides were labeled using light and heavy isotopic dimethylamine, respectively, thus enabling to verify the features based on the same ion with different labels. The results showed that the precursor ion signal from the derivatized peptide was significantly enhanced compared to that of the native peptide. And, the derived peptides could yield a variety of a, b, y, and z ions, and some reported ions in MS/MS analysis, such as the ion at m/z 129.10/135.14 produced by the peptides with glutamic acid or lysine residue at C-terminus, which facilitating to determine the C-terminal amino acid of protein. While, the peptides proned to lose the derivative groups located at the C-terminus, yielding a series of ions at m/z ［yn-45.06］ or ［yn-73.05] In addition, the neutralization of carboxyl groups could suppress the loss of phosphoryl groups in phosphopeptides to a certain extent, thus improving the resolution efficiency of the MS/MS spectra. Overall, the derivatization method based on carboxyamidation can provide abundant information for the sequence determination and quantitative analysis of peptides due to the altered fragmentation features in CID mode. [ABSTRACT FROM AUTHOR]

Post-translational modification of proteins is complex and diverse, with the phosphorylation regulated by kinases and phosphatases being one of the most widespread and important modifications. Dynamic change of quantitative analysis of phosphorylated proteins is helpful to clarify the mechanism of phosphorylation regulating life activities and understand its role in achieving biological functions. Mass spectrometry is the most commonly used strategy for the quantitative analysis of post-translational modification, involving label-free quantification, internal standard absolute quantification, and chemical labeling, etc. In this paper, a chemical labeling approach which has been used for protein glycosylation profiling was applied to the relative quantitative analysis of phosphopeptides. Using the method, carboxyl groups were located on the side chain of aspartic acid and glutamic acid residues, and the C-terminus of peptide were allowed to react with dimethylamine (d0-DMA)/deuterated dimethylamine (d6-DMA). As a result, the carboxyl groups were neutralized, and all enzymatic peptides were labeled with light/heavy tags. After the samples with different tags were mixed, the phosphopeptides were enriched using TiO2 magnetic particles and then analyzed qualitatively and relatively quantitatively by liquid chromatography-mass spectrometry (LC-MS). Amidation could shield the negatively charged carboxyl groups of non-phosphorylated and phosphorylated peptides, so that the peptides with phosphate groups mainly exhibited negative charge property, thus improving the enrichment specificity of TiO2 for phosphopeptides as well as its detection sensitivity in LC-MS analysis. Using 0.2 mg casein as a standard, 8 phosphopeptides were detected in the derivatized samples. A high abundance of b and y ions indicated that the amidation by dimethylamine was highly specific and usually occurs only at the carboxyl group without a significant effect on the phosphate group of peptides. A series of molar ratios (5∶1, 2∶1, 1∶1, 1∶2, 1∶5) of samples were derivatized using d0-DMA and d6-DMA, respectively. The results showed that the error was less than 20% for each ratio, indicating that the method possessed good relative quantitative range and accuracy. However, too many derivative sites in the peptides could result in incomplete derivatization, and the C-terminal lysine residues might self-condense to form lactam during the derivatization process. By selecting some individualized proteases during protein digestion, such as GluC, the number of derivative sites might be in an appropriate range and lysine residue could be avoided at the terminal of peptides, which should be useful for improving identification efficiency and quantitative accuracy of phosphopeptides. In summary, the chemical labeling method based on dimethylamine derivatization presents advantages for high-throughput relative quantitative analysis of phosphopeptides and it is expected to be a powerful tool for protein phosphorylation profiling in biological tissues. [ABSTRACT FROM AUTHOR]