proteotype

A proteotype is the complete set of proteins expressed by a cell, tissue, organism, or other biological system at a specific time under defined conditions. It includes not only which proteins are present but also their variants (proteoforms), post-translational modifications, abundances, and interaction states. The concept complements the ideas of genotype and phenotype, linking gene content to functional outcomes through the protein layer that executes cellular processes.

Proteotypes are dynamic and context-dependent; changes in development, environment, disease, or treatment alter the proteome. Because proteins differ by isoforms and modifications, proteotypes can reveal functional states that transcriptome alone cannot capture.

Measurement is achieved primarily by mass spectrometry-based proteomics. Approaches range from bottom-up proteomics, which infers proteins from peptides, to top-down proteomics, which analyzes intact proteoforms. Techniques such as data-dependent acquisition, data-independent acquisition, and targeted assays (MRM/PRM) produce qualitative and quantitative data, which are integrated to produce lists of identified proteins, proteoforms, post-translational modifications, and estimated abundances.

Applications include biomarker discovery, characterizing disease mechanisms, guiding therapy, and advancing systems biology and precision medicine. The proteotype provides a functional readout of cellular state that complements genomic and transcriptomic information.

Limitations and challenges include high complexity from proteoforms, incomplete proteome coverage, dynamic range, technical variability, and the need for standardized nomenclature and data formats. Ongoing developments aim to improve coverage, accuracy, and reproducibility.