Periodic Sequence Distribution of Product Ion Abundances in Electron Capture Dissociation of Amphipathic Peptides and Proteins

Hisham Ben Hamidane, Huan He, Oleg Yu Tsybin, Mark Emmett, Christopher L. Hendrickson, Alan G. Marshall, Yury O. Tsybin

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

The rules for product ion formation in electron capture dissociation (ECD) mass spectrometry of peptides and proteins remain unclear. Random backbone cleavage probability and the nonspecific nature of ECD toward amino acid sequence have been reported, contrary to preferential channels of fragmentation in slow heating-based tandem mass spectrometry. Here we demonstrate that for amphipathic peptides and proteins, modulation of ECD product ion abundance (PIA) along the sequence is pronounced. Moreover, because of the specific primary (and presumably secondary) structure of amphipathic peptides, PIA in ECD demonstrates a clear and reproducible periodic sequence distribution. On the one hand, the period of ECD PIA corresponds to periodic distribution of spatially separated hydrophobic and hydrophilic domains within the peptide primary sequence. On the other hand, the same period correlates with secondary structure units, such as α-helical turns, known for solution-phase structure. Based on a number of examples, we formulate a set of characteristic features for ECD of amphipathic peptides and proteins: (1) periodic distribution of PIA is observed and is reproducible in a wide range of ECD parameters and on different experimental platforms; (2) local maxima of PIA are not necessarily located near the charged site; (3) ion activation before ECD not only extends product ion sequence coverage but also preserves ion yield modulation; (4) the most efficient cleavage (e.g. global maximum of ECD PIA distribution) can be remote from the charged site; (5) the number and location of PIA maxima correlate with amino acid hydrophobicity maxima generally to within a single amino acid displacement; and (6) preferential cleavage sites follow a selected hydrogen spine in an α-helical peptide segment. Presently proposed novel insights into ECD behavior are important for advancing understanding of the ECD mechanism, particularly the role of peptide sequence on PIA. An improved ECD model could facilitate protein sequencing and improve identification of unknown proteins in proteomics technologies. In structural biology, the periodic/preferential product ion yield in ECD of α-helical structures potentially opens the way toward de novo site-specific secondary structure determination of peptides and proteins in the gas phase and its correlation with solution-phase structure.

Original languageEnglish (US)
Pages (from-to)1182-1192
Number of pages11
JournalJournal of the American Society for Mass Spectrometry
Volume20
Issue number6
DOIs
StatePublished - Jun 2009
Externally publishedYes

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Electrons
Ions
Peptides
Proteins
Phase structure
Amino Acids
Mass spectrometry
Modulation
Protein Sequence Analysis
Hydrophobicity
Tandem Mass Spectrometry
Hydrophobic and Hydrophilic Interactions
Proteomics
Heating
Hydrogen
Amino Acid Sequence
Mass Spectrometry
Identification (control systems)
Spine
Gases

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy

Cite this

Periodic Sequence Distribution of Product Ion Abundances in Electron Capture Dissociation of Amphipathic Peptides and Proteins. / Ben Hamidane, Hisham; He, Huan; Tsybin, Oleg Yu; Emmett, Mark; Hendrickson, Christopher L.; Marshall, Alan G.; Tsybin, Yury O.

In: Journal of the American Society for Mass Spectrometry, Vol. 20, No. 6, 06.2009, p. 1182-1192.

Research output: Contribution to journalArticle

Ben Hamidane, Hisham ; He, Huan ; Tsybin, Oleg Yu ; Emmett, Mark ; Hendrickson, Christopher L. ; Marshall, Alan G. ; Tsybin, Yury O. / Periodic Sequence Distribution of Product Ion Abundances in Electron Capture Dissociation of Amphipathic Peptides and Proteins. In: Journal of the American Society for Mass Spectrometry. 2009 ; Vol. 20, No. 6. pp. 1182-1192.
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