Proteomics and proteoforms: Bottom-up or top-down, how to use high-resolution mass spectrometry to reach the Grail

Proteomics consists of the dynamic characterization of functional proteins within a biological model in a given environment at a given time. It relies on the use of biological mass spectrometry with upstream purification/fractionation strategies. The study of proteoforms can be done by considering either these intact entities (top-down approach) or the proteolytic peptides (bottom-up approach). A partial proteolysis allows to address more specific longer peptides, for an easier study (middle-down approach). High accuracy/high resolution improves the robustness of the study of complex samples. Metadata is processed using signal processing and deconvolution algorithms for protein inference, and sequences database searching and statistical analysis. Here, we will discuss the various proteomics strategies by referring to the latest and most recent review articles at the time of writing of this text. Despite the complementarity of discussed approaches, none of which seems to allow for exhaustive coverage of the proteome.