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

Daniel P. Donnelly, Catherine M. Rawlins, Caroline J. DeHart, Luca Fornelli, Luis F. Schachner, Ziqing Lin, Jennifer L. Lippens, Krishna C. Aluri, Richa Sarin, Bifan Chen, Carter Lantz, Wonhyeuk Jung, Kendall R. Johnson, Antonius Koller, Jeremy J. Wolff, Iain D.G. Campuzano, Jared R. Auclair, Alexander R. Ivanov, Julian P. Whitelegge, Ljiljana Paša-TolićJulia Chamot-Rooke, Paul O. Danis, Lloyd M. Smith, Yury O. Tsybin, Joseph A. Loo, Ying Ge, Neil L. Kelleher, Jeffrey N. Agar*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

205 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)587-594
Number of pages8
JournalNature Methods
Issue number7
StatePublished - Jul 1 2019

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry
  • Biotechnology
  • Cell Biology


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