Proteomics has played an important role in advancing our understanding of abiotic stress response mechanisms in a wide range of crops by giving important insights into dynamic changes in protein abundance and translational and post-translational regulations. The C-termini of proteins undergo general and distinct chemical modifications that serve as recognition signatures in a variety of cellular processes, such as protein sorting, integration of proteins into membranes, regulation of protein activity, and formation of macromolecular complexes. These molecular mechanisms are partly genetically controlled but are also strongly influenced by environmental factors such as water availability and temperature, etc. In some fields there is renewed interest in analysing the C-termini of proteins in a proteome but this subfield remains largely unexplored in agronomy and crop science. Annotation of the carboxyl-terminal status of a proteome may facilitate functional classification, identification of novel proteoforms, and detection of unknown biochemical pathways. The use of C-terminal analysis has been limited so far mainly because of the technical challenge of dealing with the intrinsically low chemical reactivity of carboxyl groups. However, in recent years technological advances in mass spectrometry have made it possible to develop more efficient analytical techniques targeting C-termini. Studying the C-terminomics of plant abiotic stress responses could be a way to push forward this domain. C-terminal analysis techniques and principles developed in recent years will be reviewed and discussed here.