Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis

Abstract

Abstract. The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H] 4+ ions exhibit two major conformer types with collision cross sections of 418 Å 2 and 446 Å 2 ; the [M + 3H] 3+ ions also yield two different conformer types having collision cross sections of 340 Å 2 and 367 Å 2 . Kinetics plots of HDX for individual amino acid residues reveal fast-and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N-and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H] 3+ ions show faster HDX rate contributions compared with [M + 4H] 4+ ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H] 4+ ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

“…The hybrid instrument combining a constant-field drift tube with a linear ion trap mass spectrometer has also been described previously [17, 18, 29]. A brief description of the instrument and data collection and analysis is presented here.…”

“…Briefly, an algorithm developed in house associated each t D selection time with its resultant mass spectrum to create a three-column array file with t D , m/z , and intensity ( i ) information. From this text file, extracted ion drift time distributions (XIDTDs) [42] and extracted mass spectra could be obtained using user defined thresholds as described previously [17, 18, 29]. …”

“…Determining the amount of deuterium incorporated into specific peptide ion conformer types using the IMS-MS instrument here has been described in detail previously [17, 18, 29]. Only a brief description is provided here.…”

“…Recently, we reported the combination of a constant-field drift tube with a linear ion trap to perform IMS-HDX-MS/MS experiments [17, 18]. In these studies, dual ion gating allowed the probing of site-specific deuterium uptake for select ion conformations.…”

“…The HDX data was used to develop a model which employed site-specific deuterium uptake data to confirm mobility-matched ion structures obtained from molecular dynamics simulations (MDS)[17]. Later, site-specific HDX kinetics information was used to improve the overall efficiency of the model[18]. Notably, other important studies have used the deuterium uptake kinetics data for mechanistic studies of ion fragmentation [19].…”