Proteomiken

Proteomiken, or proteomics in its German usage, is the large-scale study of the proteins that make up a biological system. It seeks to identify which proteins are present, how abundant they are, how they modify in response to conditions, how they interact, and where they localize within cells or tissues. The proteome is dynamic and context dependent, reflecting developmental stage, environment, and disease state.

Modern proteomics relies heavily on mass spectrometry coupled with protein or peptide separation. Bottom-up, or shotgun, approaches digest proteins into peptides and identify them by tandem MS, while data-independent acquisition provides comprehensive quantification across samples. Quantification employs label-free methods or labeling strategies such as iTRAQ or TMT. Targeted proteomics uses selective reaction monitoring or parallel reaction monitoring for sensitive measurement of predefined proteins.

Proteomics has broad applications in biology and medicine, including biomarker discovery, understanding disease mechanisms, monitoring drug responses, and characterizing protein networks in health and disease. It supports systems biology, aids plant and microbial research, and enables proteogenomic studies that integrate genomic and transcriptomic data with proteome information.

Data generation is complemented by public repositories and standards. Common databases include UniProt for protein sequences and annotations and the Protein Data Bank for structures, while spectral data are deposited in repositories such as PRIDE and jPOST. Standards such as MIAPE guide reporting, and software tools like MaxQuant, Proteome Discoverer, or Skyline, support data analysis and sharing.

Challenges include the wide dynamic range of protein abundance, post-translational modifications, sample complexity, and the need for reproducible workflows. Advances such as single-cell proteomics, improved multiplexing, and integration with genomics and metabolomics hold promise for clinical translation and systems-level understanding.