Proton Dynamics in Protein Mass Spectrometry

TL;DR

This study investigates proton dynamics in protein mass spectrometry, revealing rapid proton transfer events that occur during experiments but do not significantly alter protein structures, using simulations and experimental data.

Contribution

It provides the first detailed analysis of proton transfer processes in gas-phase proteins during mass spectrometry, combining simulations with experimental validation.

Findings

Proton transfer occurs frequently during ESI-MS experiments.

Structural features of proteins are preserved despite proton dynamics.

Simulations accurately reproduce experimental charge states and collision cross sections.

Abstract

Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multi-step simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-beta peptide (Abeta(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ~0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the ps-timescale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the ms timescale). However, the structural changes associated with the process do not significantly affect the structural determinants.