The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics

Yana A. Lyon, Dylan Riggs, Luca Fornelli, Philip D. Compton, Ryan R. Julian*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. [Figure not available: see fulltext.].

Original languageEnglish (US)
Pages (from-to)150-157
Number of pages8
JournalJournal of the American Society for Mass Spectrometry
Issue number1
StatePublished - Jan 1 2018


  • HCD
  • Internal ion
  • Statistical analysis
  • UVPD

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy


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