The speciation of the proteome

Area of Science:

• Proteomics
• Biochemistry
• Molecular Biology

Background:

• Proteomics faces a paradox: proteins are known to be post-translationally modified and exist as isoforms, yet the protein expression concept often links protein names directly to function, ignoring these variations.
• This disconnect hinders a comprehensive understanding of protein function in biological systems.

Purpose of the Study:

• To highlight the limitations of current proteomics approaches in accounting for protein modifications and isoforms.
• To advocate for the adoption of the protein species concept for more accurate functional proteomics and systems biology.

Main Methods:

• Critique of bottom-up liquid chromatography/mass spectrometry (LC/MS) for peptide-level quantification, which overlooks the existence of multiple modified forms of a single peptide.
• Discussion of top-down analyses, including two-dimensional gel electrophoresis or protein liquid chromatography, as methods that separate protein species before digestion for improved discovery approaches.

Main Results:

• Bottom-up proteomics approaches fail to accurately quantify proteins due to their diverse post-translational modifications and isoforms.
• Top-down analyses enable the correlation of biological changes with protein species function by separating them before analysis.

Conclusions:

• The protein species concept is essential for meaningful quantitative analyses in functional proteomics.
• Achieving biologically relevant insights in systems biology and kinetics requires analyses at the protein species level, representing a significant challenge in contemporary proteomics.