Effect of the long-range potential on ion mobility measurements

Wyttenbach, Thomas; Helden, Gert von; Batka, Joseph J.; Carlat, Douglas; Bowers, Michael T.

doi:10.1016/s1044-0305(96)00236-x

Cited by 335 publications

(353 citation statements)

References 28 publications

Supporting

Mentioning

331

Contrasting

Order By: Relevance

“…The development of IMS instrumentation [20,[33][34][35][36][37][38][39][40], theory [41][42][43][44][45], and applications [46][47][48][49][50] is described in the literature. Here, only a brief description of the IMS-MS instrument and its operation is presented.…”

Section: Ims-ms Measurementsmentioning

confidence: 99%

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

Khakinejad

Kondalaji

Tafreshian

et al. 2015

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

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).

show abstract

Section: Ims-ms Measurementsmentioning

confidence: 99%

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

Khakinejad

Kondalaji

Tafreshian

et al. 2015

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…The freely-available, web-based Mobcal suite of modeling programs is frequently used for this purpose. Mobcal consists of three different programs: the projection approximation method originally from the Bowers' group [46] and the trajectory method and exact hard sphere scattering calculations from Jarrold [47,48]. More recent variations on the projection approximation method have emerged [36,49,50].…”

Section: Are Oligomers Amyloid Intermediates or Dead-end Products Andmentioning

confidence: 99%

“…Collision crosssections were measured directly from the IMS-MS experiment and modeling undertaken to probe potential structures of the species measured. The modeling in this case assumed each monomer to have a spherical shape and from this the average cross-sectional area was calculated using the projection approximation method [46]. Following on from this, an overlap of some 10% of monomer spheres was found to reproduce the experimental cross-sectional area of the dimer, and this adjustment was used to model the higher-order oligomers in this study.…”

Section: Are Oligomers Amyloid Intermediates or Dead-end Products Andmentioning

confidence: 99%

Mass spectrometry and the amyloid problem—How far can we go in the gas phase?

Ashcroft

2010

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

A number of proteins are capable of converting from their soluble, monomeric form into highlyordered, insoluble aggregates known as amyloid fibrils. In vivo, these fibrils, which accumulate in organs and tissues, are associated with a wide range of amyloid diseases for which there are currently no therapeutic solutions. The molecular details of the pathway from native monomer through oligomeric intermediates to the final amyloid fibril remain a challenging enigma. Over the past few years, mass spectrometry has been applied to investigate the various stages of amyloid fibril formation, and this report summarizes the key steps achieved to date. (J Am Soc Mass Spectrom 2010, 21, 1087-1096

show abstract

“…The theoretical cross section of an each structure was calculated using the SIGMA 'project approximation' algorithm with atomic radii determined from the ion-helium Lennard-Jones parameters. [23,24] Average cross section was obtained from the candidate group. The conformational stability of the lowest energy structure (representative structure) was then tested with a 1ns MD simulation at 300 K.…”

Section: Molecular Modelling and Theoretical Cross Sectionsmentioning

confidence: 99%

Non‐covalent interactions of alkali metal cations with singly charged tryptic peptides

Rožman

Gaskell

2010

J. Mass Spectrom.

View full text Add to dashboard Cite

The complexes formed by alkali metal cations (Cat + = Li + ,Na + ,K + ,Rb + ) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M+H +Cat] 2+ tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li + or Na + ) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb + ) is cation expulsion and formation of [M + H] + . The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M+H+Cat] 2+ ion. Finally, the fact that [M+H+Cat] 2+ peptides dissociate similarly as [M + H] + (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.

show abstract

Effect of the long-range potential on ion mobility measurements

Cited by 335 publications

References 28 publications

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

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

Mass spectrometry and the amyloid problem—How far can we go in the gas phase?

Non‐covalent interactions of alkali metal cations with singly charged tryptic peptides

Contact Info

Product

Resources

About