Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry

Morsa, Denis; Hanozin, Emeline; Eppe, Gauthier; Quinton, Loïc; Gabelica, Valérie; Pauw, Edwin De

doi:10.1021/acs.analchem.9b05850

Cited by 56 publications

(137 citation statements)

References 64 publications

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“…In addition, TIMS experiments as a function of the trapping time (100–500 ms) did not evidence any unfolding events for the [M + 6H] 6+ ions of ubiquitin but only a small narrowing of the IMS band (Figure S4c and Table S3). This means that the effective temperature in the TIMS analyzer is not high enough to induce unfolding which deviates from the observations previously reported for the case of proteins and are more in adequation with the observations reported by Bleiholder et al…”

Section: Resultscontrasting

confidence: 78%

“…In addition, TIMS experiments as a function of the trapping time (100−500 ms) did not evidence any unfolding events for the [M + 6H] 6+ ions of ubiquitin but only a small narrowing of the IMS band (Figure S4c and Table S3). This means that the effective temperature in the TIMS analyzer is not high enough to induce unfolding which deviates from the observations previously reported for the case of proteins 48 and are more in adequation with the observations reported by Bleiholder et al 49 Native Macromolecular Assemblies in a Convex TIMS Geometry. The analysis of native concanavalin A (ConA), a homotetramer of 103 kDa, resulted in the observation of the native IMS and MS profiles consisting of a single IMS band per charge state over the [M + 17H] 17+ −[M + 21H] 21+ range (Figure 3a).…”

Section: ■ Results and Discussioncontrasting

confidence: 78%

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Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies

et al. 2021

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The structural elucidation of native macromolecular assemblies has been a subject of considerable interest in native mass spectrometry (MS), and more recently in tandem with ion mobility spectrometry (IMS-MS), for a better understanding of their biochemical and biophysical functions. In the present work, we describe a new generation trapped ion mobility spectrometer (TIMS), with extended mobility range (K 0 = 0.185−1.84 cm 2 •V −1 •s −1 ), capable of trapping high-molecular-weight (MW) macromolecular assemblies. This compact 4 cm long TIMS analyzer utilizes a convex electrode, quadrupolar geometry with increased pseudopotential penetration in the radial dimension, extending the mobility trapping to high-MW species under native state (i.e., lower charge states). The TIMS capabilities to perform variable scan rate (Sr) mobility measurements over short time (100−500 ms), high-mobility resolution, and ion-neutral collision cross-section (CCS N 2 ) measurements are presented. The trapping capabilities of the convex electrode TIMS geometry and ease of operation over a wide gas flow, rf range, and electric field trapping range are illustrated for the first time using a comprehensive list of standards varying from CsI clusters (n = 6−73), Tuning Mix oligomers (n = 1−5), common proteins (e.g., ubiquitin, cytochrome C, lysozyme, concanavalin (n = 1−4), carbonic anhydrase, β clamp (n = 1−4), topoisomerase IB, bovine serum albumin (n = 1−3), topoisomerase IA, alcohol dehydrogenase), IgG antibody (e.g., avastin), protein−DNA complexes, and macromolecular assemblies (e.g., GroEL and RNA polymerase (n = 1−2)) covering a wide mass (up to m/z 19 000) and CCS range (up to 22 000 Å 2 with <0.6% relative standard deviation (RSD)).

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Section: Resultscontrasting

confidence: 78%

Section: ■ Results and Discussioncontrasting

confidence: 78%

Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies

et al. 2021

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“…Collision-induced unfolding as a technique is still relatively new; however, early examples show it may provide insight, for example, in the study of protein–ligand binding ( 54 ). Unintentional ion heating can occur while injecting ions into, or while holding ions in, the TIMS analyzer ( 55 , 56 , 57 ). During injection, the DC field in the entrance funnel is of principle concern.…”

Section: Timsmentioning

confidence: 99%

Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics

Meier

Park

Mann

2021

Molecular & Cellular Proteomics

111

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Recent advances in efficiency and ease of implementation have rekindled interest in ion mobility spectrometry, a technique that separates gas phase ions by their size and shape and that can be hybridized with conventional LC and MS. Here, we review the recent development of trapped ion mobility spectrometry (TIMS) coupled to TOF mass analysis. In particular, the parallel accumulation–serial fragmentation (PASEF) operation mode offers unique advantages in terms of sequencing speed and sensitivity. Its defining feature is that it synchronizes the release of ions from the TIMS device with the downstream selection of precursors for fragmentation in a TIMS quadrupole TOF configuration. As ions are compressed into narrow ion mobility peaks, the number of peptide fragment ion spectra obtained in data-dependent or targeted analyses can be increased by an order of magnitude without compromising sensitivity. Taking advantage of the correlation between ion mobility and mass, the PASEF principle also multiplies the efficiency of data-independent acquisition. This makes the technology well suited for rapid proteome profiling, an increasingly important attribute in clinical proteomics, as well as for ultrasensitive measurements down to single cells. The speed and accuracy of TIMS and PASEF also enable precise measurements of collisional cross section values at the scale of more than a million data points and the development of neural networks capable of predicting them based only on peptide sequences. Peptide collisional cross section values can differ for isobaric sequences or positional isomers of post-translational modifications. This additional information may be leveraged in real time to direct data acquisition or in postprocessing to increase confidence in peptide identifications. These developments make TIMS quadrupole TOF PASEF a powerful and expandable platform for proteomics and beyond.

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“…41 This raises concern when performing nMS experiments, in which maintaining the native-like structure and avoiding unintentional activation is of critical importance. 21,43,44 It has since been clarified that that ion heating likely occurs due to non-intrinsic properties of TIMS (space charge effects and RF power absorption) and that careful tuning prevents structural rearrangement, therefore making TIMS a suitable technology for nMS. 44 For the experiments performed in this manuscript, the amplitude of the RF-confining voltage in the TIMS funnel was set as low as possible, while still trapping a sufficient amount of ions, and trapping times in the TIMS analyzer were kept low to limit structural perturbation.…”

Section: Tims-cid and Tims-sid Of Cholera Toxin B Pentamer (With Gm1 mentioning

confidence: 99%

Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry

Panczyk¹,

Snyder²,

Ridgeway³

et al. 2020

Preprint

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<p><a>Native mass spectrometry, particularly in conjunction with gas-phase ion mobility spectrometry measurements, has proven useful as a structural biology tool for evaluating the stoichiometry, conformation, and topology of protein complexes. Here, we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer for structural analysis of protein complexes. We successfully performed SID on mobility-selected protein complexes, including streptavidin tetramer and cholera toxin B with bound ligand. Additionally, TIMS-SID was employed on a mixture of peptides bradykinin desR1 and desR9 to mobility separate and identify the individual peptides. Importantly, results show that native-like conformations can be maintained throughout the TIMS analysis. The TIMS-SID spectra are analogous to SID spectra acquired using quadrupole mass selection, indicating little measurable, if any, structural rearrangement during mobility selection. Mobility parking was used on the ion or mobility of interest and 50 to 200 SID mass spectra were averaged. High quality TIMS-SID spectra were acquired over a period of 2-10 minutes, comparable to or slightly longer than SID coupled with ion mobility on various instrument platforms in our laboratory. The ultrahigh resolving power of the 15 T FT-ICR allowed for the identification and relative quantification of overlapping SID fragments with the same nominal <i>m/z</i> based on isotope patterns and shows promise as a platform to probe small mass differences, such as protein-ligand binding or post-translational modifications. These results represent the potential of TIMS-SID-MS for the analysis of both protein complexes and peptides.</a></p>

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Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry

Cited by 56 publications

References 64 publications

Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies

Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies

Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics

Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry

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