Proteoms

Proteoms, or proteomes, are the complete complement of proteins expressed by a genome, cell, tissue, or organism under specific conditions. A proteome encompasses protein sequences, their isoforms, and post-translational modifications, as well as associations into complexes. Proteomes are dynamic and vary across developmental stages, environmental stimuli, and disease states.

Proteomics is the field that studies proteomes at scale, integrating experimental measurements with computational analysis. Common approaches rely on mass spectrometry coupled with chromatography to identify and quantify proteins in complex mixtures. Quantitative methods include labeling techniques such as iTRAQ or TMT and label-free approaches. Data processing assigns proteins to spectra, estimates abundance, and infers modifications and interactions.

Applications of proteomics and proteome analysis include biomarker discovery, mapping signaling networks, characterizing disease mechanisms, and guiding drug development. Large-scale efforts profile many organisms and tissues to build reference proteomes and compare conditions. Public resources supporting proteome data include UniProt for protein sequences and annotations, and ProteomeXchange, PRIDE, PeptideAtlas, and related databases for deposited mass spectrometry data.

Challenges in proteome characterization include the wide dynamic range of protein abundance, extensive post-translational modifications, and the presence of isoforms that complicate identification. Coverage is often incomplete, requiring complementary methods and ongoing standardization. Despite these hurdles, proteome-level information remains central to systems biology and translational research.