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.