ProteomEbene

ProteomEbene, often rendered in German as Proteom-Ebene, is a conceptual layer in systems biology that refers to the complete set of proteins expressed by a cell, tissue, or organism under specific conditions. It includes not only protein abundance but also proteoforms arising from alternative splicing, post-translational modifications, and proteolytic processing, as well as subcellular localization and interaction networks. The ProteomEbene serves as a functional intermediary between the genome and the phenotypic state, translating genetic information into cellular activity.

Measurement and analysis of the ProteomEbene rely on proteomics technologies, primarily mass spectrometry. Workflows typically involve protein extraction, enzymatic digestion, and LC-MS/MS analysis, followed by peptide identification and quantitative inference. Quantification can be label-free or use isobaric labeling approaches (such as TMT or iTRAQ), and results are mapped to proteins while accounting for proteoforms and inference from peptide data. Data processing includes quality control, normalization, and statistical assessment, as well as integration with other omics layers to build a coherent biological picture.

Applications and challenges: The ProteomEbene is central to biomarker discovery, understanding disease mechanisms, and informing drug discovery by revealing altered protein pathways and interactions. Challenges include incomplete proteome coverage, technical variability, handling proteoforms, and integrating proteomic data with transcriptomic and metabolomic information. Reproducibility and cross-platform comparability remain active areas of methodological development.

Outlook: Advances in quantitative, spatial, and single-cell proteomics, along with improved data standards and multi-omics integration, are expanding the depth and precision of the ProteomEbene, enabling more detailed models of cellular function and disease.