proteome

A proteome is the complete set of proteins that can be expressed by a cell, tissue, organism, or biological system under a defined condition or time. It reflects the proteins that are translated and present, including their abundance, isoforms, and post-translational modifications.

Proteomes are highly dynamic, varying across cell types, developmental stages, and in response to stimuli or disease. Proteoforms describe the different molecular forms a protein can take due to genetic variation, alternative splicing, and post-translational modifications such as phosphorylation, glycosylation, and ubiquitination.

Proteomics studies the proteome through technologies such as mass spectrometry, chromatography, and gel-based separation, often coupled with labeling strategies or label-free quantification. Common approaches include shotgun proteomics, targeted proteomics (for example MRMs/SRM), and data-independent acquisition (DIA or SWATH).

Key resources include protein sequence databases and proteomics repositories that support data sharing and standards, such as UniProt, the Protein Data Bank, PRIDE, and the Proteomics Standards Initiative. Large-scale efforts like the Human Proteome Project aim to map the human proteome across tissues and conditions.

Proteomics informs biomarker discovery, drug target identification, and systems biology, complementing genomics and transcriptomics. Challenges include the wide dynamic range of protein abundance, diverse post-translational modifications, and achieving reproducibility across platforms and laboratories.