Enriching C-terminal peptide from endopeptidase ArgC digest for protein C-terminal analysis

Negative enrichment strategy combined with site-specific derivatization for the C-terminomics

Protein C-termini containing valuable biological information plays a vital role in various physiological processes, such as protein localization, protein recognition, and signal transduction in organisms. However, C-terminal peptide identification is still challenging due to their low abundance and similar physicochemical properties to other digested peptides. Herein, we developed a simple and mild strategy for the enrichment of C-terminal peptides that incorporates selectively 2-pyridinecarbaldehyde (2-PCA) derivatization of α-amine with negative enrichment by NHS resin. Two synthesized peptides were utilized to evaluate the efficiency of 2-PCA derivatization and optimize the coupling conditions of NHS resin. The feasibility of the method was further validated by enriching the C-terminus of the bovine serum albumin (BSA). Finally, this method was successfully applied to the C-terminus analysis of mouse brain tissue, identifying 404 protein C-termini with physicochemical properties unbiasedly. Additionally, the GO and KEGG analyses revealed that these identified proteins are crucial for proper brain function. In summary, our proposed method is effective and has the potential to facilitate comprehensive C-terminal analysis of proteins. SIGNIFICANCE: Effective enrichment methods are essential for the identification of the proteins C-terminus. In this study, a mild and simple method for negative C-terminal enrichment combined with site-specific derivatization was developed. The enrichment process was simplified and minimized sample loss simultaneously, using 2-PCA derivatization which has high α-amino specificity. Up to 346C-terminal proteins were identified in mouse brain tissue unbiasedly and reliably. This approach has the potential to facilitate comprehensive analysis of protein C-termini in a variety of biological contexts.

Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics

Gel-free bottom-up shotgun proteomics is the principal methodological platform for the state-of-the-art proteome research. This methodology assumes quantitative isolation of the total protein fraction from a complex biological sample, its limited proteolysis with site-specific proteases, analysis of the resulted peptides with nanoscaled reversed-phase high-performance liquid chromatography-(tandem) mass spectrometry (nanoRP-HPLC-MS and MS/MS), protein identification by sequence database search and peptide-based quantitative analysis. The most critical steps of this workflow are protein reconstitution and digestion; therefore, detergents and chaotropic agents are strongly mandatory to ensure complete solubilization of complex protein isolates and to achieve accessibility of all protease cleavage sites. However, detergents are incompatible with both RP separation and electrospray ionization (ESI). Therefore, to make LC-MS analysis possible, several strategies were implemented in the shotgun proteomics workflow. These techniques rely either on enzymatic digestion in centrifugal filters with subsequent evacuation of the detergent, or employment of MS-compatible surfactants, which can be degraded upon the digestion. In this review we comprehensively address all currently available strategies for the detergent-assisted proteolysis in respect of their relative efficiency when applied to different biological matrices. We critically discuss the current progress and the further perspectives of these technologies in the context of its advances and gaps.

An Approach to Incorporate Multi-Enzyme Digestion into C-TAILS for C-Terminomics Studies

Protein C-termini study is still a challenging task and far behind its counterpart, N-termini study. MS based C-terminomics study is often hampered by the low ionization efficiency of C-terminal peptides and the lack of efficient enrichment methods. We previously optimized the C-terminal amine-based isotope labeling of substrates (C-TAILS) method and identified 369 genuine protein C-termini in Escherichia coli. A key limitation of C-TAILS is that the prior protection of amines and carboxylic groups at protein level makes Arg-C as the only specific enzyme in practice. Herein, we report an approach combining multi-enzyme digestion and C-TAILS, which significantly increases the identification rate of C-terminal peptides and consequently improves the applicability of C-TAILS in biological studies. We carry out a systematic study and confirm that the omission of the prior amine protection at protein level has a negligible influence and allows the application of multi-enzyme digestion. We successfully apply five different enzyme digestions to C-TAILS, including trypsin, Arg-C, Lys-C, Lys-N, and Lysarginase. As a result, we identify a total of 722 protein C-termini in E. coli, which is at least 66% more than the results using any single enzyme. Moreover, the favored enzyme and enzyme combination are discovered. Data are available via ProteomeXchange with identifier PXD004275.

Fishing the PTM proteome with chemical approaches using functional solid phases

Currently available chemical approaches for the enrichment and separation of a PTM proteome using functional solid phases were reviewed.

C-terminomics: Targeted analysis of natural and posttranslationally modified protein and peptide C-termini

The C-terminus (where C is carboxyl) of a protein can serve as a recognition signature for a variety of biological processes, including protein trafficking and protein complex formation. Hence, the identity of the in vivo protein C-termini provides valuable information about biological processes. Analysis of protein C-termini is also crucial for the study of C-terminal PTMs, particularly for monitoring proteolytic processing by endopeptidases and carboxypeptidases. Although technical difficulties have limited the study of C-termini, a range of technologies have been proposed in the last couple of years. Here, we review the current proteomics technologies for C-terminal analysis, with a focus on the biological information that can be derived from C-terminomics studies.