Proteomics goes native

When scientists analyze proteins with mass spectrometry, they typically denature the biomolecules, causing the proteins’ biologically relevant forms and composition to disappear. In contrast, so-called native mass spectrometry allows proteins and their complexes to remain intact during analysis.

For the past 15 years, though, native mass spectrometry has been relegated to analyzing specific, targeted protein complexes rather than unknown mixtures of them, says Neil L. Kelleher, a professor of chemistry at Northwestern University.

Now a team of researchers led by Kelleher and Northwestern’s Philip D. Compton has expanded native mass spectrometry into native proteomics, which they can use in an untargeted discovery mode to analyze endogenous complexes in cells and tissues (Nat. Chem. Biol. 2017, DOI: 10.1038/nchembio.2515). “This technique represents the next step in the evolution of native MS,” Kelleher says.

In their new method, the researchers extract protein complexes from cells and tissue, separate them, and analyze them by native top-down mass spectrometry. The native conditions preserve interactions that would be lost in harsher conditions. The team characterized 125 intact protein complexes and 217 distinct protein molecular species, including posttranslational modifications (PTMs), extracted from mouse heart and human cancer cell lines.

For example, the researchers observed a previously unreported Mg²⁺ binding site in a dimer of the human α-enolase enzyme. The binding site wasn’t present on the enzyme monomer. The team was also able to identify sequence variations and PTMs of cysteines on protein surfaces, which are often lost in denaturing proteomics.

The work is “impressive,” says Joseph A. Loo, a biochemistry professor at UCLA who also uses native mass spectrometry. “Their experimental platform contributes additional value to the typical proteomics output by adding information on ligand binding, PTMs, and functional assemblies.”