Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry

  • Nicole A. Haverland
  • Owen S. Skinner
  • Ryan T. Fellers
  • Areeba A. Tariq
  • Bryan P. Early
  • Richard D. LeDuc
  • Luca Fornelli
  • Philip D. Compton
  • Neil L. Kelleher
Research Article


Fragmentation of intact proteins in the gas phase is influenced by amino acid composition, the mass and charge of precursor ions, higher order structure, and the dissociation technique used. The likelihood of fragmentation occurring between a pair of residues is referred to as the fragmentation propensity and is calculated by dividing the total number of assigned fragmentation events by the total number of possible fragmentation events for each residue pair. Here, we describe general fragmentation propensities when performing top-down mass spectrometry (TDMS) using denaturing or native electrospray ionization. A total of 5311 matched fragmentation sites were collected for 131 proteoforms that were analyzed over 165 experiments using native top-down mass spectrometry (nTDMS). These data were used to determine the fragmentation propensities for 399 residue pairs. In comparison to denatured top-down mass spectrometry (dTDMS), the fragmentation pathways occurring either N-terminal to proline or C-terminal to aspartic acid were even more enhanced in nTDMS compared with other residues. More generally, 257/399 (64%) of the fragmentation propensities were significantly altered (P ≤ 0.05) when using nTDMS compared with dTDMS, and of these, 123 were altered by 2-fold or greater. The most notable enhancements of fragmentation propensities for TDMS in native versus denatured mode occurred (1) C-terminal to aspartic acid, (2) between phenylalanine and tryptophan (F|W), and (3) between tryptophan and alanine (W|A). The fragmentation propensities presented here will be of high value in the development of tailored scoring systems used in nTDMS of both intact proteins and protein complexes.

Graphical Abstract


Native mass spectrometry Top-down mass spectrometry Residue fragmentation propensity Fragmentation propensity Native electrospray ionization Native ESI Tandem mass spectrometry 



The authors acknowledge the W. M. Keck foundation for generous support and funding (DT061512). In addition, this work was partially supported by R01GM067193 (NIGMS). O.S.S. was supported by an NSF graduate research fellowship (2014171659).

Supplementary material

13361_2017_1635_MOESM1_ESM.xlsx (71 kb)
ESM 1 (XLSX 71 kb)


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Copyright information

© American Society for Mass Spectrometry 2017

Authors and Affiliations

  • Nicole A. Haverland
    • 1
  • Owen S. Skinner
    • 1
  • Ryan T. Fellers
    • 1
  • Areeba A. Tariq
    • 1
  • Bryan P. Early
    • 1
  • Richard D. LeDuc
    • 1
  • Luca Fornelli
    • 1
  • Philip D. Compton
    • 1
  • Neil L. Kelleher
    • 1
  1. 1.Department of Chemistry and Molecular Biosciences and the Proteomics Center of ExcellenceNorthwestern UniversityEvanstonUSA

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