Charge location directs electron capture dissociation of peptide dications

Abstract

The effect of peptide dication charge location on electron capture dissociation (ECD) fragmentation pattern is investigated. ECD fragmentation patterns are compared for peptides with amide and free acid C-terminal groups. ECD of free acid compared with C-terminally amidated peptides with basic residues near the N-terminus demonstrates increased formation of a-type ions. Similarly, ECD of free acid compared with C-terminally amidated peptides with basic residues near the C-terminus exhibits increased formation of y-type ions. Alteration of the peptide sequence to inhibit the formation of charged side chains (i.e., amino acid substitution and acetylation) provides further evidence for charge location effect on ECD. We propose that formation of zwitterionic peptide structures increases the likelihood of amide nitrogen protonation (versus basic side chains), which is responsible for the increase in a-and y-type ion formation. (J Am Soc Mass Spectrom 2006, 17, 1704 -1711

Electron capture and transfer dissociation: Peptide structure analysis at different ion internal energy levels

“…ETD directly followed by autoCRCID of singly charged species of charge-reduced radical ions generates a typical ECD FT-ICR MS type mass spectrum of Substance P with z 9 and most c ions present (c 4 -c 10 ) (Figure 1, top) [19,37]. As expected [32], ETD without CRCID produced an incomplete set of c ions ranging from c 6 to c 10 ( Figure 1, middle).…”

“…Particular advances have been achieved as a result of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)-based electron capture dissociation (ECD) [4] complementarity to slow heating fragmentation methods [5], such as collision-induced dissociation (CID) [6] and infrared multiphoton dissociation (IRMPD) [7]. In addition to mainly product ion mass-based MS/ MS, product ion abundance (PIA) in ECD is increasingly considered as a new source of information to improve peptide and protein sequencing [8,9], quantitative modification analysis [10,11], higher-order structure characterization [8,[12][13][14][15], providing new insights into ECD mechanism [16,17], suggesting charge location in peptides and proteins [18,19], and indicating routes toward developing a quantitative model of ECD/ETD [15]. Double-resonance (DR) ECD, with and without ion preactivation, is used to estimate the radical intermediate lifetimes and differentiate between short-lived and long-lived intermediates by monitoring PIA variation attributed to radical intermediates ejection from the ICR trap immediately upon formation [20,21].…”

Periodic sequence distribution of product ion abundances in electron capture dissociation of amphipathic peptides and proteins

“…The 9.4 T FT-ICR MS was operated as follows. After 1 to 2 s accumulation and precursor ion selection in the external octopole ion trap, ions were transported by a radiofrequency octopole ion guide into an openended cylindrical ICR trap [17]. Gated ion trapping was used without cooling gas.…”

“…ECD FT-ICR MS of six doubly protonated horse myoglobin tryptic fragments ( [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16], [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31], [32][33][34][35][36][37][38][39][40][41][42] Figure S2) and with vibrational activation ( Figure 5) confirm preferential and sometimes periodic product ion formation from peptides with mainly ␣-helical or ␤-turn secondary structure in solution (before protein digestion). Predominantly z-ions are observed because of preferential charge retention at the C-terminal Lys or Arg basic residue upon electron capture, as expected for doubly charged tryptic peptides.…”

“…Supplementary Figure S2 demonstrates preferential cleavage at the NOC ␣ bond number 4 (z nϪ3 ) for fragments with a distinct ␣-helical or turn structure at the N-terminus (fragments [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16], [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] -118]). The periodicity is more pronounced in AI-ECD data ( Figure 5), demonstrating a period of 3 amino acids for the specified myoglobin fragments.…”