protéomes

The protéome is the entire set of proteins expressed by a genome, cell, tissue, or organism at a given time under specific conditions. Unlike the static genome, the proteome reflects cellular state and environment, as proteins are produced, modified, and degraded in a dynamic balance. Proteomes include different isoforms and post-translationally modified proteoforms that influence function and localization.

Proteoforms: A single gene can generate multiple proteoforms through alternative splicing, proteolytic processing, and post-translational modifications. The concept emphasizes functional diversity; measuring a protein at the level of the gene product requires proteomics to capture isoforms and modifications.

Proteomics is the study of proteomes using experimental and computational methods. The dominant approach is mass spectrometry, often coupled with liquid chromatography (LC-MS/MS), to identify and quantify proteins in complex samples. Complementary approaches include gel-based separation (2D-PAGE) and affinity-based techniques. Quantification uses label-free methods or labeling strategies such as TMT or iTRAQ.

Data resources and challenges: Proteome data are stored in repositories such as UniProt for protein sequences, and proteomics databases like PRIDE and ProteomicsDB. Challenges include the wide dynamic range of protein abundance, detection of low-abundance proteins, and accurate localization and quantification of post-translational modifications.

Applications: Proteomics informs biology and medicine, enabling biomarker discovery, elucidation of disease mechanisms, and the identification of drug targets. Integrated with genomics and transcriptomics, proteomics contributes to systems biology and personalized medicine.