Basic Strong Cation Exchange Chromatography, BaSCX, a Highly Efficient Approach for C‑Terminomic Studies Using LysargiNase Digestion

Decoding protein
C-termini is a challenging task in protein chemistry
using conventional chemical and enzymatic approaches. With the rapid
development in modern mass spectrometer, many advanced mass spectrometry
(MS)-based protein C-termini analysis approaches have been established.
Although great progress is being continually achieved, it is still necessary to develop more efficient
approaches in order to discover a proteome-scale protein C-termini
(C-terminome) and consequently to help understand their biological
functions. In this report, we describe the BaSCX method, for basic strong cation exchange chromatography, for C-terminome
studies. Taking advantage of carboxylic amidation, LysargiNase digestion,
and optimized search parameters, BaSCX enables identification of 1806
and 1812 database-annotated human protein C-termini from HeLa and
293T cells, resepctively, by triplicate experiments using 40 μg
proteins each. Combined together, 2151 human protein C-termini, nearly
three times the recently reported largest human C-terminome data set,
are reported in this study. Similar results were acquired in different
organisms, including mice, C. elegans, and tomatoes. Furthermore, we report for the first time the discovery
of C-terminal-specific modifications using a proteomic approach, including
three methyl-esterified protein C-termini and 16 α-amidated
protein C-termini, demonstrating the excellent performance and great
potential of BaSCX in C-terminomic studies. Data are available via
ProteomeXchange with identifier PXD016317.