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Mass spectrometry

Raw protein from the top down

Nature Chemistry volume 10, pages 114–116 (2018)Cite this article

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Mass spectrometry is a powerful technique for analysing proteins, yet linking higher-order protein structure to amino acid sequence and post-translational modifications is far from simple. Now, a native top-down method has been developed that can provide information on higher-order protein structure and different proteoforms at the same time.

Protein mass spectrometry is commonly associated with large-scale, high-throughput proteomics studies, during which small pieces of the proteins under study (∼2 kDa peptides from protein digestion by proteases such as trypsin) are introduced into, and subsequently fragmented in, the mass spectrometer for determination of peptide and peptide fragment mass values. Widespread application of this 'bottom-up' mass spectrometry approach has been made possible by various instrumental, methodological and computational developments during the past two decades1 that have enabled routine protein identification, quantitation and the localization of post-transcriptional modifications (PTMs) within the peptides2. However, bottom-up mass spectrometry relies on protein denaturation and digestion into peptides before mass spectrometry analysis, which eliminates important correlations between amino acid sequence, PTMs and higher-order structure. In contrast, 'top-down' and 'native' mass spectrometry methods do not involve protein digestion and have been developed for obtaining information on primary and higher-order protein structure, respectively. The major difference between the three approaches lies in how the protein is treated before introduction into the mass spectrometer, similar to the different ways in which protein can be prepared for food: denatured and digested (bottom-up mass spectrometry), denatured (top-down mass spectrometry) or raw (native mass spectrometry). Now, writing in Nature Chemistry, a team led by Huilin Li and Joseph A. Loo report an integrated top-down and native mass spectrometry approach that provides information on both primary and quaternary protein structure3.

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Figure 1: Native top-down mass spectrometry of protein complexes.

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  1. Institute of Organic Chemistry and the Center for Molecular Biosciences Innsbruck (CMBI) at the University of Innsbruck, Innrain 80/82, Innsbruck, 6020, Austria

    Kathrin Breuker

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  1. Kathrin Breuker
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Correspondence to Kathrin Breuker.

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Breuker, K. Raw protein from the top down. Nature Chem 10, 114–116 (2018). https://doi.org/10.1038/nchem.2936

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