Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation.
Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions. Graphical Abstract ᅟ.
C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
Mahdiar
M
Khakinejad
C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
Samaneh
S
Ghassabi Kondalaji
Department of Statistics, West Virginia University, P.O. Box 6330, Morgantown, WV, 26506, USA.
Amirmahdi
A
Tafreshian
C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA. stephen.valentine@mail.wvu.edu.
Stephen J
SJ
Valentine
D000595:Amino Acid Sequence; D003903:Deuterium / Q000737:chemistry; D041961:Deuterium Exchange Measurement / Q000379:methods; D005740:Gases / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*
D005740:Gases; D007477:Ions; D010455:Peptides; D006859:Hydrogen; D003903:Deuterium
Collision cross-section measurements; Gas-phase hydrogen/deuterium exchange; Hydrogen/deuterium exchange