Scientific Context: Proteins, Key Players in Life and Pillars of Modern Research

Proteins play a crucial role in most biological processes. Their function is primarily correlated with their molecular structure, in addition to their subcellular localization. Mass spectrometry has become an indispensable tool for proteomic studies that utilize genomic data to describe the protein content of a model in correlation with a specific functional pathway. The term "proteome" appeared in the literature in 1995. It is defined as the complete set of proteins in a genome and largely involves mass spectrometry (MS) techniques. However, the study of proteomes began more than 20 years earlier with 2D gel electrophoresis. The discovery of two new soft ion sources for mass spectrometry in the mid-1980s, MALDI and ESI, has certainly led to the exponential development of proteomic studies, as they were immediately associated with direct applications to the analysis of polypeptides and small proteins.

Describing protein function and understanding their malfunctions is a major challenge for environmental and biomedical life sciences. In this perspective, studying protein molecular diversity is essential to identify the different molecular forms of a protein encoded by a gene and not just the protein itself. Protein modifications reflect many interdependent phenomena, such as point mutations on the primary sequence, alternative splicing, or post-translational modifications (PTMs) that are covalently added to the primary sequence or proteolytic events during maturation. These PTMs regulate protein function, as is the case, for example, of glycosylation for antibodies and phosphorylation for signaling cascades.

The number of proteoforms results from their combinatorial nature. If the number of human coding sequences is around 20,000, there are several million potential proteoforms. Today, proteomics has reached a stage where the quantitative analysis of functional proteoforms and the stoichiometry of each modification (the modification rate of each modified site) have become a major research axis. This is the ultimate level for deciphering biological functions.