Carboxypeptidase B-assisted charge-based fractional diagonal chromatography for deep screening of C-terminome

ABSTRACT: The determination of protein C-termini is of great significance for protein function annotation and proteolysis re-search. However, the progress of C-terminomics is still far behind its counterpart, N-terminomics, because of the low reactivity of the carboxyl group. Herein, we developed a negative selection strategy, termed carboxypeptidase B-assisted charge-based fractional diagonal chromatography (CPB-ChaFRADIC), to achieve a global C-terminome analysis. The highly reactive carboxypeptidase B cleavage was utilized to reduce the charge state of non-C-terminal peptides. Together with high-performance charge-based frac-tional diagonal chromatography, the C-terminal peptides could be isolated. Such a strategy was also applied for profiling C-termini from Escherichia coli cell lysates, and 441 canonical C-termini and 510 neo-C-termini originating from proteolytic processing were identified. These findings represent 2-fold and 5.8-fold that of identified C-termini via direct analysis, respectively. Using parallel digestion with trypsin and LysC, such a strategy enabled the identification of 604 canonical C-termini and 818 neo-C-termini, rep-resenting the largest C-terminome dataset of E. coli, and no deficiency in His/Lys/Arg-containing C-terminal peptides was observed. The presented CPB-ChaFRADIC strategy is therefore a highly efficient and unbiased strategy for large-scale C-terminome analysis. Furthermore, using the CPB-ChaFRADIC strategy, we identified 87 cleavage sites and 82 substrates of caspase-3 in Jurkat cells, demonstrating that the CPB-ChaFRADIC strategy shows great promise in promoting proteolysis research.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Escherichia Coli

TISSUE(S): Cell Suspension Culture, Cell Culture, Jurkat Cell

SUBMITTER: Lingfan Chen  

LAB HEAD: Lihua Zhang

PROVIDER: PXD018520 | Pride | 2020-05-25

REPOSITORIES: Pride