The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Abstract

Molecular dynamics (MD) is an essential tool for correlating collision cross-section data determined by ion mobility spectrometry (IMS) with candidate (calculated) structures. Conventional methods used for ion structure determination rely on comparing the measured cross-sections with the calculated collision cross-section for the lowest energy structure(s) taken from a large pool of candidate structures generated through multiple tiers of simulated annealing. We are developing methods to evaluate candidate structures from an ensemble of many conformations rather than the lowest energy structure. Here, we describe computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH 2 -Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI, and compare the structures of MIFAGIK derivatives to test the 'sensitivity' of the cluster analysis method. Cluster analysis suggests that [MIFAGIK ϩ H] ϩ ions formed by MALDI have a predominantly turn structure even though the low-energy ions prefer partial helical conformers. T he emphasis of mass spectrometry based biological chemistry is shifting from compound identification to structural studies of large biomolecules and biomolecule complexes [1][2][3][4][5][6][7], including membrane proteins [8]. The next phase of 'omics' related research must be aimed at obtaining and predicting additional dimensions of information, such as secondary, tertiary, and quaternary structures and linkage-specific information for glycans. Although sophisticated structural characterization tools, such as NMR and XRD, provide the most information, high throughput analysis of complex biological mixtures obtained by using these techniques is an underdeveloped technology. On the other hand, IMS is much more than a separation device, the structural information derived from 2D conformation space afforded by IM-MS is potentially well-suited to both high throughput applications and complex biological samples.A number of laboratories have focused their research on developing IM-MS for biophysical studies of peptides and proteins [9 -14]. In previous work, we showed that a large proportion of singly charged peptide ions (formed by MALDI) appear on a single trendline in 2D mobility-m/z plots, i.e., plots of arrival-time distribution (ATD) or ion-neutral collision cross-section (⍀) versus m/z [15]; however, a few ion signals deviate (Ͼ3% to ϳ20%) from the expected trendline and nonpeptidic ion signals appear on separate, compound class specific trendlines [14,15]. Ruotolo et al. showed that gas-phase [M ϩ H] ϩ ions of LLGNVLVVVLAR (derived from bovine hemoglobin) prefer extended (helical) structure(s) resulting in a larger collision cross-section than random coil structures having the same or similar m/z values [12,13], while some post-translationally modified (PTM) peptide ions (phosphopeptides) tend to pack more tightly than the unmodified protonated peptide ions owing to intra-molecular charge-solvation and/or formation of salt-...

Ion Mobility Collision Cross Section Compendium

“…The large blue bubble in Figure 7 corresponds to the 8676 peptide cross sections published by Smith and coworkers in 2010 in support of developing theoretical methods for predicting the IM drift time based upon the primary amino acid sequence. 72 While most of the CCS values have been for tryptic peptides, there is recent and significant efforts being made in the quantitative IM analysis of structurally-interesting peptide and protein classes, including helical peptides, 174–176 metalloproteins, 177–180 intrinsically-disordered proteins, 181–184 metamorphic proteins, 185,186 amyloids, 187–194 and membrane-bound proteins and assemblies. 117,195–198 The last three years has seen a balance of cross section reporting across most of the chemical classes, including lipids and carbohydrates.…”

Activation State-Selective Kinase Inhibitor Assay Based on Ion Mobility-Mass Spectrometry

“…To assess finer protein tertiary structure details, IM-MS datasets must be combined with sophisticated MD simulations. 13 Since many protein folds project identical CCS values, the information content carried by the IM-MS experiment necessarily decreases as the size of the protein increases, and the structural filtering requirements of the MD simulations utilized are greatly enhanced. Despite this inherent limitation, the structures of many small proteins have been determined in this fashion, including the desolvated structures for ubiquitin 14 and Aβ 1–42 .…”

Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study

“…With larger ions, structures are usually obtained by force-field molecular dynamics calculations and converted to Ω th by a method not using ion–molecule potentials. 12–14 This approach has the disadvantage of not using equilibrium geometries for gas-phase ions and not considering intermolecular interaction potentials between the ion and the gas molecules. The DFT-TM approach has been shown to produce Ω th within a few percent of the experimental Ω for several peptide ions.…”

“…The DFT-TM approach has been shown to produce Ω th within a few percent of the experimental Ω for several peptide ions. 15,16 However, an inherent weakness of DFT-TM is that it uses 0 K equilibrium structures to approximate the properties of gas-phase ions in experiments that are performed at ambient or elevated temperatures 12–14 where a number of peptide vibrational modes are active. Vibrational effects on ion drift mobilities have been studied for rigid ion structures such as C 60 and found to be weak.…”