Automation of C-terminal sequence analysis of 2D-PAGE separated proteins

•We provided a proof-of-concept of a chemical selection method for C-terminal peptide detection on MALDI-TOF MS.•We automated the chemical method for C-terminal sequencing on a robotic station.•We show that the method is amenable for identification of proteins from non-model organisms.

Experimental assignment of the protein termini remains essential to define the functional protein structure. Here, we report on the improvement of a proteomic C-terminal sequence analysis method. The approach aims to discriminate the C-terminal peptide in a CNBr-digest where Met-Xxx peptide bonds are cleaved in internal peptides ending at a homoserine lactone (hsl)-derivative. pH-dependent partial opening of the lactone ring results in the formation of doublets for all internal peptides. C-terminal peptides are distinguished as singlet peaks by MALDI-TOF MS and MS/MS is then used for their identification. We present a fully automated protocol established on a robotic liquid-handling station.

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