Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

Daniel Donnelly (1) , Catherine Rawlins (1) , Caroline Dehart (2) , Luca Fornelli (2) , Luis Schachner (2) , Ziqing Lin (3) , Jennifer Lippens (4) , Krishna Aluri (1, 5) , Richa Sarin (1) , Bifan Chen (3) , Carter Lantz (6) , Wonhyeuk Jung (6) , Kendall Johnson (1) , Antonius Koller (1) , Jeremy Wolff (7) , Iain Campuzano (4) , Jared Auclair (1) , Alexander Ivanov (1) , Julian Whitelegge (6) , Ljiljana Paša-Tolić (8) , Julia Chamot-Rooke (9) , Paul Danis , Lloyd Smith (3) , Yury Tsybin (10) , Joseph Loo (6) , Ying Ge (3) , Neil Kelleher (2) , Jeffrey Agar (1)

1 Northeastern University [Boston]
2 Northwestern University [Evanston]
3 University of Wisconsin-Madison
4 Amgen Inc. [Thousand Oaks, CA, USA]
5 Alnylam Pharmaceuticals
6 UCLA - University of California [Los Angeles]
7 Bruker Daltonics
8 PNNL - Pacific Northwest National Laboratory
9 UTechS MSBio - Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology
10 Spectroswiss

One gene can give rise to many functionally distinct proteoforms, each of which has a characteristic molecular mass. Top-down mass spectrometry enables the analysis of intact proteins and proteoforms. Here members of the Consortium for Top-Down Proteomics provide a decision tree that guides researchers to robust protocols for mass analysis of intact proteins (antibodies, membrane proteins and others) from mixtures of varying complexity. We also present cross-platform analytical benchmarks using a protein standard sample, to allow users to gauge their proficiency.

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology

Daniel Donnelly, Catherine Rawlins, Caroline Dehart, Luca Fornelli, Luis Schachner, et al.. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature Methods, 2019, 16 (7), pp.587-594. ⟨10.1038/s41592-019-0457-0⟩. ⟨pasteur-02331018⟩