The proteome is defined as the set of proteins expressed in an organism, tissue, cell, biological fluid, organelle under given conditions and at a given time (Mark Wilkins, 1994). Unlike the genome, the proteome is dynamic, and its study elucidates many biological processes. It is important to note that proteins are direct products of genes, that a genetic sequence can produce several protein products, and each of them can undergo various post-translational modifications. Together, these numerous proteoforms (estimated to be over a million in humans) reflect cellular function and explain biological complexity.
Proteomic analysis by mass spectrometry is currently the most effective method for obtaining maximum information about the proteins composing a biological sample. It can provide numerous pieces of information such as protein abundance, protein-protein interactions or with other molecules, the presence of post-translational modifications, subcellular localization, etc.
It is also important to note that unlike gene expression analysis by transcriptomics (RNA seq), proteomics provides access to proteins, which are the final effectors of genes. It has been demonstrated that there is a low correlation between protein expression levels and mRNA levels because the efficiency of translation and the half-life of mRNA and proteins can have a significant impact on the proteome content.
By allowing the identification and quantification of thousands of proteins from less than 1µg of protein extract in less than an hour, proteomic analysis by mass spectrometry has become an essential tool in many fields: biology, diagnostics, microbiology, toxicology, biotechnology, nutrition, etc.