S.O. is thankful to the French National Research Agency for funding his Ph.D. (grant ANR-18-CE29-0006).

The authors have no conflict of interest to disclose.

The SELECT SERIES Cyclic IMS is a powerful tool that allows selecting a defined ion population&#8212;of a given m/z and ion mobility&#8212;without the need for upstream chromatographic separation. The instrument affords the possibility of generating a bidimensional fragmentation map of this ion population, from which both MS/MS and IMS/IMS spectra can be extracted. However, the user must note several critical points that require attention during the experimental process.
First, the us...

The complete chemical characterization of biomolecules is key to understanding their underlying biological and functional properties. To this end, &#34;omics&#34; sciences have developed in recent years, aiming for the large-scale characterization of chemical structures at biological concentrations. In proteomics and metabolomics, MS has become a core tool to unravel the structural heterogeneity found in biological media-notably thanks to its sensitivity and ability to provide structural information through tandem MS (MS/MS). In MS/MS strategies, an ion is selected according to its mass, then fragmented, and finally, the masses of its fragments are acquired to establish a fingerprint of the molecule. MS/MS spectra can, in particular, be used to match spectral databases1,2, or tentatively reconstruct the parent structures3,4. Under the assumption that similar spectra belong to similar compounds, MS/MS data can also be used to build molecular networks (MNs) connecting related species through a similarity score5,6.
However, because of the inherent property of MS to detect the mass-to-charge ratio (m/z) of ions, the technique is blind to a number of structural features that fall within the range of (stereo)isomerism. For example, carbohydrates are made of several monosaccharide subunits, many of which are stereoisomers or even epimers (e.g., Glc vs. Gal or Glc vs. Man). These subunits are linked by glycosidic bonds, which can differ by the position of the linkage (regioisomerism) and the steric configuration of the anomeric carbon (anomerism). These characteristics make it difficult for standalone MS to distinguish between carbohydrate isomers7, and only regioisomerism can be addressed using high-energy activation methods8,9,10. Although derivatization is an option to disrupt the equivalence of stereoisomeric groups11, it requires extensive sample preparation. Another, more straightforward option is to couple MS with an analytical dimension sensitive to isomerism, such as IMS.
Because this protocol is designed for users who are already familiar with the basic concepts of IMS, and because detailed reviews are available elsewhere12,13, only a brief overview of the principles of IMS is given here. IMS is a gas-phase separation method that relies on the interaction of ions with a buffer gas and an electric field, ultimately separating ions according to their gas-phase conformations. Different principles of IMS coupled to MS can be found on commercial instruments: some operate at alternating high and low electric fields (field asymmetric IMS, FAIMS), while most operate within the low field limit&#8212;notably drift tube IMS (DTIMS, linearly decreasing electric field), traveling wave IMS (TWIMS, symmetric potential waves), and trapped IMS (TIMS, high flow of buffer gas trapping ions against electric fields)13. The low-field methods allow access to a so-called CCS, a property of the ion-gas pair that represents the surface (in &#197;2 or nm2) of the ion that interacts with the buffer gas during the separation. CCS is theoretically instrument-independent and is thus useful to generate data that can be reproduced between different laboratories14. Ion mobility separations can be impacted by various parameters and, notably, by fluctuations of the gas pressure and gas temperature in the mobility cell. The CCS calibration is a way to remedy this, as both the calibrant and the species of interest will be similarly affected13. However, it is mandatory to install the instrument in a temperature-controlled room and to have a reliable gas pressure control system.
An interesting evolution of IMS is IMS/IMS, which was first introduced in 2006 by Clemmer&#39;s group as an analog of MS/MS15,16. In IMS/IMS, an ion of interest is selectively isolated based on its ion mobility; it is then activated (until possible fragmentation), and a new IMS analysis of the activated ion or fragments is performed. In the first instrumental design, two IMS cells were put in series, separated by an ion funnel where the activation stood. Since then, although a number of IMS/IMS setups were proposed (for a review, see Eldrid and Thalassinos17), the first commercial mass spectrometer with IMS/IMS capability only became available in 201918. This instrument substantially improved the initial concept by combining it with another technological breakthrough: a cyclic design of the IMS cell.
The cyclic IMS cell theoretically allows increasing near-infinitely the drift path length and, thus, the resolving power of the instrument19. This was achieved by means of a particular instrument geometry, where the cyclic TWIMS cell is placed orthogonally to the main ion optical axis. A multifunction array region at the entrance of the IMS cell allows controlling the direction of the ion path: (i) sending ions sideways for IMS separation, (ii) forward for MS detection, or (iii) backward from the IMS cell to be stored in a prearray cell. From this prearray store cell, the ions can be activated and the fragments reinjected in the IMS cell for ion mobility measurement, an approach that has been successfully used to characterize stereoisomers20. Ultimately, the collected data contain ion mobility and m/z information for the precursor and its fragments.
In a recent publication that used this cyclic design for glycan analyses (Ollivier et al.21), we showed that the mobility profile of the fragments contained in such IMS/IMS data acts as a fingerprint of a biomolecule that can be used in a molecular networking strategy. The resulting network, called IM-MN, led to the organization of glycomics datasets in a structurally relevant way, whereas the network built solely from MS/MS data (MS-MN) revealed little information. To complement this publication and help Cyclic IMS users implement this workflow, this protocol provides a complete description of the protocol used to collect the data. This protocol focuses only on the generation of the IMS/IMS data that users can then use to build IM-MN networks (see21)&#8212;or for any other application of their choice. Building of IM-MN will not be considered herein, as protocols for molecular networking are already available22. The crucial points that must be followed to generate valuable and reproducible IMS/IMS acquisitions are highlighted. Taking the example of one of the oligosaccharides studied by Ollivier et al.21, the following steps are detailed: (i) sample preparation, (ii) tuning of the Cyclic IMS instrument, (iii) automated peak-picking of the data, and (iv) CCS calibration.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>33-&#945;-L- plus 23-&#945;-L-Arabinofuranosyl-xylotetraose (XA3XX/XA2XX) mixture</td>
			<td>Megazyme Ltd., Wicklow, Ireland</td>
			<td>O-XAXXMIX</td>
			<td>XA2XX + XA3XX mixture</td>
		</tr>
		<tr>
			<td>33-&#945;-L-Arabinofuranosyl-xylotetraose (XA3XX)</td>
			<td>Megazyme Ltd., Wicklow, Ireland</td>
			<td>O-XA3XX</td>
			<td>Pure XA3XX standard</td>
		</tr>
		<tr>
			<td>Eppendorf Safe-Lock Tubes, 1.5 mL, Eppendorf Quality, colorless, 1,000 tubes</td>
			<td>Eppendorf, Hamburg, Germany</td>
			<td>0030120086</td>
			<td>Used to prepare the carbohydrate stock solution and dilution</td>
		</tr>
		<tr>
			<td>FALCON 50 mL Polypropylene Conical Tube 30 x 115 mm</td>
			<td>Corning Science M&#233;xico S.A. de C.V., Reynosa, Tamaulipas, Mexico</td>
			<td>352070</td>
			<td>Used to prepare the aqueous stock solution of 100 mM LiCl</td>
		</tr>
		<tr>
			<td>Lithium Chloride (ACS reagent, &#8805;99 %)</td>
			<td>Sigma-Aldrich Inc., Saint Quentin Fallavier, France</td>
			<td>310468</td>
			<td>Used to dope the sample with lithium</td>
		</tr>
		<tr>
			<td>Major Mix IMS/Tof Calibration Kit</td>
			<td>Waters Corp., Wilmslow, UK</td>
			<td>186008113</td>
			<td>Calibration solution for MS and IMS</td>
		</tr>
		<tr>
			<td>MassLynx 4.2 SCN1016 Release 6 (Waters Embedded Analyser Platform for Cyclic IMS 2.9.1 Release 9)</td>
			<td>Waters Corp., Wilmslow, UK</td>
			<td>721022377</td>
			<td>Cyclic IMS vendor software for instrument control and data processing</td>
		</tr>
		<tr>
			<td>Methanol for HPLC PLUS Gradient grade</td>
			<td>Carlo-Erba Reagents, Val de Reuil, France</td>
			<td>412383</td>
			<td>High-purity solvent</td>
		</tr>
		<tr>
			<td>MS Leucine Enkephaline Kit</td>
			<td>Waters Corp., Wilmslow, UK</td>
			<td>700002456</td>
			<td>Reference compound used for tuning of the mass spectrometer</td>
		</tr>
		<tr>
			<td>SCHOTT DURAN 100 mL borosilicate glass bottle</td>
			<td>VWR INTERNATIONAL, Radnor, Pennsylvania, US</td>
			<td>218012458</td>
			<td>Used to prepare the solution of 500 &#181;M LiCl in 50:50 MeOH/Water</td>
		</tr>
		<tr>
			<td>SELECT SERIES Cyclic IMS</td>
			<td>Waters Corp., Wilmslow, UK</td>
			<td>186009432</td>
			<td>Ion mobility-mass spectrometer equipped with a cylic IMS cell</td>
		</tr>
		<tr>
			<td>Website: http://mzmine.github.io/</td>
			<td>MZmine Development Team</td>
			<td>-</td>
			<td>Link to download the MZmine software</td>
		</tr>
		<tr>
			<td>Website: https://github.com/siollivier/IM-MN</td>
			<td>INRAE, UR BIA, BIBS Facility, Nantes, France</td>
			<td>-</td>
			<td>Link to an in-house R script containing a CCS calibration function</td>
		</tr>
	</tbody>
</table>

using a cyclic ion mobility spectrometer for tandem ion mobility experiments

Accurate characterization of chemical structures is important to understand their underlying biological mechanisms and functional properties. Mass spectrometry (MS) is a popular tool but is not always sufficient to completely unveil all structural features. For example, although carbohydrates are biologically relevant, their characterization is complicated by numerous levels of isomerism. Ion mobility spectrometry (IMS) is an interesting complement because it is sensitive to ion conformations and, thus, to isomerism. 
Furthermore, recent advances have significantly improved the technique: the last generation of Cyclic IMS instruments offers additional capabilities compared to linear IMS instruments, such as an increased resolving power or the possibility to perform tandem ion mobility (IMS/IMS) experiments. During IMS/IMS, an ion is selected based on its ion mobility, fragmented, and reanalyzed to obtain ion mobility information about its fragments. Recent work showed that the mobility profiles of the fragments contained in such IMS/IMS data can act as a fingerprint of a particular glycan and can be used in a molecular networking strategy to organize glycomics datasets in a structurally relevant way. 
The goal of this protocol is thus to describe how to generate IMS/IMS data, from sample preparation to the final Collision Cross Section (CCS) calibration of the ion mobility dimension that yields reproducible spectra. Taking the example of one representative glycan, this protocol will show how to build an IMS/IMS control sequence on a Cyclic IMS instrument, how to account for this control sequence to translate IMS arrival time into drift time (i.e., the effective separation time applied to the ions), and how to extract the relevant mobility information from the raw data. This protocol is designed to clearly explain the critical points of an IMS/IMS experiment and thus help new Cyclic IMS users perform straightforward and reproducible acquisitions.

An arabinoxylan pentasaccharide, XA2XX, was chosen as an example to illustrate this protocol. This compound is commercially available, but only as a mixture with another arabinoxylan pentasaccharide, XA3XX (pure XA3XX is also commercially available). The structures of XA2XX and XA3XX are given in Supplemental&#160;Figure S1. As the ratio of XA2XX and XA3XX in the commercial mixture is ~50:50, a solution at 20 &#181;g/mL of the m...

Watch this Scientific Journal Video about Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments at JoVE.com

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Ion mobility spectrometry (IMS) is an interesting complement to mass spectrometry for the characterization of biomolecules, notably because it is sensitive to isomerism. This protocol describes a tandem IMS (IMS/IMS) experiment, which allows the isolation of a molecule and the generation of the mobility profiles of its fragments.

Accurate characterization of chemical structures is important to understand their underlying biological mechanisms and functional properties. Mass ...

using-cyclic-ion-mobility-spectrometer-for-tandem-ion-mobility

Research

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Chemistry

4.1K Views.  INRAE, UR BIA, F-44316 Nantes, France. Ion mobility spectrometry (IMS) is an interesting complement to mass spectrometry for the characterization of biomolecules, notably because it is sensitive to isomerism. This protocol describes a tandem IMS (IMS/IMS) experiment, which allows the isolation of a molecule and the generation of the mobility profiles of its fragments. 

Video: Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Analyzing the Photo-oxidation of 2-propanol at Indoor Air Level Concentrations Using Field Asymmetric Ion Mobility Spectrometry

We demonstrate a versatile protocol to be used for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) volatile organic carbons (VOCs), illustrating this with a titanium dioxide based catalyst, and the VOC 2-propanol. The protocol takes advantage of field asymmetric ion mobility spectroscopy (FAIMS), an analysis tool that is capable of continuously identifying and monitoring the concentration of VOCs such as 2-propanol and acetone at the ppb level. The continuous nature of FAIMS allows detailed kinetic analysis, and long-term reactions, offering a significant advantage over gas chromatography, a batch process traditionally used in air purification characterization. The use of FAIMS in photocatalytic air purification has only recently been used for the first time, and with the protocol illustrated here, the flexibility in allowing alternative VOCs and photocatalysts to be tested using comparable protocols offers a unique system to elucidate photocatalytic air purification reactions at low concentrations.

A protocol for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) model volatile organic carbons such as 2-propanol is described.

We demonstrate a versatile protocol to be used for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) volatile ...

An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry

The analysis of low-level (1-100 ppm) protein impurities (e.g., host-cell proteins (HCPs)) in protein biotherapeutics is a challenging assay requiring high sensitivity and a wide dynamic range. Mass spectrometry-based quantification assays for proteins typically involve protein digestion followed by the selective reaction monitoring/multiple reaction monitoring (SRM/MRM) quantification of peptides using a low-resolution (Rs ~1,000) tandem quadrupole mass spectrometer. One of the limitations of this approach is the interference phenomenon observed when the peptide of interest has the "same" precursor and fragment mass (in terms of m/z values) as other co-eluting peptides present in the sample (within a 1-Da window). To avoid this phenomenon, we propose an alternative mass spectrometric approach, a high selectivity (HS) MRM assay that combines the ion mobility separation of peptide precursors with the high-resolution (Rs ~30,000) MS detection of peptide fragments. We explored the capabilities of this approach to quantify low-abundance peptide standards spiked in a monoclonal antibody (mAb) digest and demonstrated that it has the sensitivity and dynamic range (at least 3 orders of magnitude) typically achieved in HCP analysis. All six peptide standards were detected at concentrations as low as 0.1 nM (1 femtomole loaded on a 2.1-mm ID chromatographic column) in the presence of a high-abundance peptide background (2 &#181;g of a mAb digest loaded on-column). When considering the MW of rabbit phosphorylase (97.2 kDa), from which the spiked peptides were derived, the LOQ of this assay is lower than 50 ppm. Relative standard deviations (RSD) of peak areas (n = 4 replicates) were less than 15% across the entire concentration range investigated (0.1-100 nM or 1-1,000 ppm) in this study.

Here, we describe a chromatographic assay coupled with the ion mobility separation of peptide precursors followed by the high-resolution (~30,000) MS-detection of peptide fragments for the quantification of spiked peptide standards in a monoclonal antibody digest.

The analysis of low-level (1-100 ppm) protein impurities (e.g., host-cell proteins (HCPs)) in protein biotherapeutics is a challenging assay requiring ...

A Practical Guide on Coupling a Scanning Mobility Sizer and Inductively Coupled Plasma Mass Spectrometer (SMPS-ICPMS)

A large variety of analytical methods are available to characterize particles in aerosols and suspensions. The choice of the appropriate technique depends on the properties to be determined. In many fields information about particle size and chemical composition are of great importance. While in aerosol techniques particle size distributions of gas-borne particles are determined online, their elemental composition is commonly analyzed offline after an appropriate sampling and preparation procedure. To obtain both types of information online and simultaneously, a hyphenated setup was recently developed, including a Scanning Mobility Particle Sizer (SMPS) and an Inductively Coupled Plasma Mass Spectrometer (ICPMS). This allows first to classify the particles with respect to their mobility diameter, and then to determine their number concentration and elemental composition in parallel. A Rotating Disk Diluter (RDD) is used as the introduction system, giving more flexibility regarding the use of different aerosol sources. In this work, a practical guide is provided describing the different steps for establishing this instrumentation, and how to use this analysis tool. The versatility of this hyphenated technique is demonstrated in example measurements on three different aerosols generated out of a) a salt solution, b) a suspension, and c) emitted by a thermal process.

A Practical Guide on Coupling a Scanning Mobility Sizer and Inductively Coupled Plasma Mass Spectrometer SMPS-ICPMS

In this work a practical guide is provided, describing the different steps to establish the coupling of SMPS and ICPMS systems, and how to use them. Three descriptive examples are presented.

A large variety of analytical methods are available to characterize particles in aerosols and suspensions. The choice of the appropriate technique depends ...

Membrane Remodeling of Giant Vesicles in Response to Localized Calcium Ion Gradients

In a wide variety of fundamental cell processes, such as membrane trafficking and apoptosis, cell membrane shape transitions occur concurrently with local variations in calcium ion concentration. The main molecular components involved in these processes have been identified; however, the specific interplay between calcium ion gradients and the lipids within the cell membrane is far less known, mainly due to the complex nature of biological cells and the difficultly of observation schemes. To bridge this gap, a synthetic approach is successfully implemented to reveal the localized effect of calcium ions on cell membrane mimics. Establishing a mimic to resemble the conditions within a cell is a severalfold problem. First, an adequate biomimetic model with appropriate dimensions and membrane composition is required to capture the physical properties of cells. Second, a micromanipulation setup is needed to deliver a small amount of calcium ions to a particular membrane location. Finally, an observation scheme is required to detect and record the response of the lipid membrane to the external stimulation. This article offers a detailed biomimetic approach for studying the calcium ion-membrane interaction, where a lipid vesicle system, consisting of a giant unilamellar vesicle (GUV) connected to a multilamellar vesicle (MLV), is exposed to a localized calcium gradient formed using a microinjection system. The dynamics of the ionic influence on the membrane were observed using fluorescence microscopy and recorded at video frame rates. As a result of the membrane stimulation, highly curved membrane tubular protrusions (MTPs) formed inside the GUV, oriented away from the membrane. The described approach induces the remodeling of the lipid membrane and MTP production in an entirely contactless and controlled manner. This approach introduces a means to address the details of calcium ion-membrane interactions, providing new avenues to study the mechanisms of cell membrane reshaping.

We present a technique for contactless micromanipulation of vesicles, using localized calcium ion gradients. Microinjection of a calcium ion solution, in the vicinity of a giant lipid vesicle, is utilized to remodel the lipid membrane, resulting in the production of membrane tubular protrusions.

In a wide variety of fundamental cell processes, such as membrane trafficking and apoptosis, cell membrane shape transitions occur concurrently with local ...

Imaging Corrosion at the Metal-Paint Interface Using Time-of-Flight Secondary Ion Mass Spectrometry

Corrosion developed at the paint and aluminum (Al) metal-paint interface of an aluminum alloy is analyzed using time-of-flight secondary ion mass spectrometry (ToF-SIMS), illustrating that SIMS is a suitable technique to study the chemical distribution at a metal-paint interface. The painted Al alloy coupons are immersed in a salt solution or exposed to air only. SIMS provides chemical mapping and 2D molecular imaging of the interface, allowing direct visualization of the morphology of the corrosion products formed at the metal-paint interface and mapping of the chemical after corrosion occurs. The experimental procedure of this method is presented to provide technical details to facilitate similar research and highlight pitfalls that may be encountered during such experiments.

Time-of-flight secondary ion mass spectrometry is applied to demonstrate the chemical mapping and corrosion morphology at the metal-paint interface of an aluminum alloy after being exposed to a salt solution compared with a specimen exposed to air.

Corrosion developed at the paint and aluminum (Al) metal-paint interface of an aluminum alloy is analyzed using time-of-flight secondary ion mass ...

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, metal-binding interactions, and conformational shape. Coupling ESI with ion mobility-mass spectrometry (IM-MS) provides an instrumental technique that allows for simultaneous measurement of a peptide&#8217;s mass-to-charge (m/z) and collision cross section (CCS) that relate to its stoichiometry, protonation state, and conformational shape. The overall charge of a peptide complex is controlled by the protonation of 1) the peptide&#8217;s acidic and basic sites and 2) the oxidation state of the metal ion(s). Therefore, the overall charge state of a complex is a function of the pH of the solution that affects the peptides metal ion binding affinity. For ESI-IM-MS analyses, peptide and metal ions solutions are prepared from aqueous-only solutions, with the pH adjusted with dilute aqueous acetic acid or ammonium hydroxide. This allows for pH dependence and metal ion selectivity to be determined for a specific peptide. Furthermore, the m/z and CCS of a peptide complex can be used with B3LYP/LanL2DZ molecular modeling to discern binding sites of the metal ion coordination and tertiary structure of the complex. The results show how ESI-IM-MS can characterize the selective chelating performance of a set of alternative methanobactin peptides and compare them to the copper-binding peptide methanobactin.

Ion mobility-mass spectrometry and molecular modeling techniques can characterize the selective metal chelating performance of designed metal-binding peptides and the copper-binding peptide methanobactin. Developing new classes of metal chelating peptides will help lead to therapeutics for diseases associated with metal ion misbalance.

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, ...

3D Depth Profile Reconstruction of Segregated Impurities Using Secondary Ion Mass Spectrometry

The presented protocol combines excellent detection limits (1 ppm to 1 ppb) using secondary ion mass spectrometry (SIMS) with reasonable spatial resolution (~1 &#181;m). Furthermore, it describes how to obtain realistic three-dimensional (3D) distributions of segregated impurities/dopants in solid state materials. Direct 3D depth profile reconstruction is often difficult to achieve due to SIMS-related measurement artifacts. Presented here is a method to identify and solve this challenge. Three major issues are discussed, including the i) nonuniformity of the detector being compensated by flat-field correction; ii) vacuum background contribution (parasitic oxygen counts from residual gases present in the analysis chamber) being estimated and subtracted; and iii)&#160;performance of all steps within a stable timespan of the primary ion source. Wet chemical etching is used to reveal the position and types of dislocation in a material, then the SIMS result is superimposed on images obtained via scanning electron microscopy (SEM). Thus, the position of agglomerated impurities can be related to the position of certain defects. The method is fast and does not require sophisticated sample preparation stage; however, it requires a high-quality, stable ion source, and the entire measurement must be performed quickly to avoid deterioration of the primary beam parameters.

The presented method describes how to identify and solve measurement artifacts related to secondary ion mass spectrometry as well as obtain realistic 3D distributions of impurities/dopants in solid state materials.

The presented protocol combines excellent detection limits (1 ppm to 1 ppb) using secondary ion mass spectrometry (SIMS) with reasonable spatial ...

Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes Using Ion Mobility-Mass Spectrometry

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry (ES-IM-MS) and energy-resolved threshold collision-induced dissociation (TCID) to measure the thermochemistry of the dissociation of negatively-charged [amb+M(II)+NTA]- ternary complexes into two product channels: [amb+M(II)] + NTA or [NTA+M(II)]-&#160;+ amb, where M = Zn or Ni and NTA is nitrilotriacetic acid. The complexes contain one of the alternative metal binding (amb) heptapeptides with the primary structures acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 or acetyl-Asp1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7, where the amino acids&#39; Aa1,2,6,7 positions are the potential metal-binding sites. Geometry-optimized stationary states of the ternary complexes and their products were selected from quantum chemistry calculations (presently the PM6 semi-empirical Hamiltonian) by comparing their electronic energies and their collision cross-sections (CCS) to those measured by ES-IM-MS. From the PM6 frequency calculations, the molecular parameters of the ternary complex and its products model the energy-dependent intensities of the two product channels using a competitive TCID method to determine the threshold energies of the reactions that relate to the 0 K enthalpies of dissociation (&#916;H0). Statistical mechanics thermal and entropy corrections using the PM6 rotational and vibrational frequencies provide the 298 K enthalpies of dissociation (&#916;H298). These methods describe an EI-IM-MS routine that can determine thermochemistry and equilibrium constants for a range of ternary metal ion complexes.

Thermochemical Studies of NiII and ZnII Ternary Complexes Using Ion Mobility-Mass Spectrometry

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry, semi-empirical quantum calculations, and energy-resolved threshold collision-induced dissociation to measure the relative thermochemistry of the dissociation of related ternary metal complexes.

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry (ES-IM-MS) and energy-resolved threshold ...

Histone Proteomic Analysis and Post-Translational Modification Characterization

Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry

Histone proteins are highly abundant and conserved among eukaryotes and play a large role in gene regulation as a result of structures known as posttranslational modifications (PTMs). Identifying the position and nature of each PTM or pattern of PTMs in reference to external or genetic factors allows this information to be statistically correlated with biological responses such as DNA transcription, replication, or repair. In the present work, a high-throughput analytical protocol for the detection of histone PTMs from biological samples is described. The use of complementary liquid chromatography, trapped ion mobility spectrometry, and time-of-flight mass spectrometry (LC-TIMS-ToF MS/MS) enables the separation and PTM assignment of the most biologically relevant modifications in a single analysis. The described approach takes advantage of recent developments in dependent data acquisition (DDA) using parallel accumulation in the mobility trap, followed by sequential fragmentation and collision-induced dissociation. Histone PTMs are confidently assigned based on their retention time, mobility, and fragmentation pattern.

Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF

An analytical workflow based on liquid chromatography, trapped ion mobility spectrometry, and time-of-flight mass spectrometry (LC-TIMS-ToF MS/MS) for high confidence and highly reproducible "bottom-up" analysis of histone modifications and identification based on principal parameters (retention time [RT], collision cross section [CCS], and accurate mass-to-charge [m/z] ratio).