title: Charge site mass spectra: conformation-sensitive components of the electron capture dissociation spectrum of a protein.
abstract: A conventional electron capture dissociation (ECD) spectrum of a protein is uniquely characteristic of the first dimension of its linear structure. This sequence information is indicated by summing the primary c (m+) and z (m+•) products of cleavage at each of its molecular ion's inter-residue bonds. For example, the ECD spectra of ubiquitin (M + nH)(n+) ions, n = 7-13, provide sequence characterization of 72 of its 75 cleavage sites from 1843 ions in seven c ((1-7)+) and eight z ((1-8)+•) spectra and their respective complements. Now we find that each of these c/z spectra is itself composed of "charge site (CS)" spectra, the c (m+) or z (m+•) products of electron capture at a specific protonated basic residue. This charge site has been H-bonded to multiple other residues, producing multiple precursor ion forms; ECD at these residues yields the multiple products of that CS spectrum. Closely similar CS spectra are often formed from a range of charge states of ubiquitin and KIX ions; this indicates a common secondary conformation, but not the conventional α-helicity postulated previously. CS spectra should provide new capabilities for comparing regional conformations of gaseous protein ions and delineating ECD fragmentation pathways.
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Owen S
authors.initials: OS
authors.lastname: Skinner
authors.forename: Kathrin
authors.initials: K
authors.lastname: Breuker
authors.forename: Fred W
authors.initials: FW
authors.lastname: McLafferty
mesh_terms: D004583:Electrons; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry
chemical_list: D007477:Ions; D011506:Proteins; D025801:Ubiquitin
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