Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode

Luis F. Schachner, Denise P. Tran, Alexander S. Lee, John P. McGee, Kevin Jooss, Kenneth R. Durbin, Henrique S. Seckler, Lauren Adams, Erika N. Cline, Rafael D. Melani, Ashley N. Ives, Benjamin Des Soye, Neil L. Kelleher, Steven M. Patrie

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


The combined use of electrospray ionization run in so-called “native mode” with top-down mass spectrometry (nTDMS) is enhancing both structural biology and discovery proteomics by providing three levels of information in a single experiment: the intact mass of a protein or complex, the masses of its subunits and non-covalent cofactors, and fragment ion masses from direct dissociation of subunits that capture the primary sequence and combinations of diverse post-translational modifications (PTMs). While intact mass data are readily deconvoluted using well-known software options, the analysis of fragmentation data that result from a tandem MS experiment – essential for proteoform characterization – is not yet standardized. In this tutorial, we offer a decision-tree for the analysis of nTDMS experiments on protein complexes and diverse bioassemblies. We include an overview of strategies to navigate this type of analysis, provide example data sets, and highlight software for the hypothesis-driven interrogation of fragment ions for localization of PTMs, metals, and cofactors on native proteoforms. Throughout we have emphasized the key features (deconvolution, search mode, validation, other) that the reader can consider when deciding upon their specific experimental and data processing design using both open-access and commercial software.

Original languageEnglish (US)
Article number116591
JournalInternational Journal of Mass Spectrometry
StatePublished - Jul 2021
Externally publishedYes


  • Bioinformatics
  • Decision-tree
  • Fragment analysis
  • Native mass spectrometry
  • Native top-down mass spectrometry
  • Tandem MS

ASJC Scopus subject areas

  • Instrumentation
  • Condensed Matter Physics
  • Spectroscopy
  • Physical and Theoretical Chemistry


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