Recommendations for reporting ion mobility mass spectrometry measurements

© 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc

SLIM Tricks: Tools, Concepts, and Strategies for the Development of Planar Ion Guides

Traveling wave ion mobility experiments using planar electrode structures (e.g., structures for lossless ion manipulation, TW-SLIM) leverage the mature manufacturing capabilities of printed circuit boards (PCBs). With routine levels of mechanical precision below 150 μm, the conceptual flexibility afforded by PCBs for use as planar ion guides is expansive. To date, the design and construction of TW-SLIM platforms require considerable legacy expertise, especially with respect to simulation and circuit layout strategies. To lower the barrier of TW-SLIM implementation, we introduce Python-based interactive tools that assist in graphical layout of the core electrode footprints for planar ion guides with minimal user inputs. These scripts also export the exact component locations and assignments for direct integration into KiCad and SIMION for PCB finalization and ion flight simulations. The design concepts embodied in the set of scripts comprising SLIM Pickins (PCB CAD generation) and pigsim (SIMION workspace generation) build upon the lessons learned in the independent development of the research-grade TW-SLIM platforms in operation at WSU. Due to the inherent flexibility of the PCB manufacturing process and the time devoted to board layouts prior to manufacturing, both scripts serve to enable rapid, iterative design considerations. Because only a few predefined parameters are necessary (i.e., the TW-SLIM monomer width, x position following a TW Turn, and y position following a TW Turn) it is possible to design the exact component layouts and accompanying simulation space in a manner of minutes. There is no known limitation to the board layout capacities of the scripts, and the size of a designed layout is ultimately constrained by the abilities of the final PCB design and simulation tools, KiCad and SIMION, to accommodate the thousands of electrodes comprising the final design (i.e., RAM and software overhead). Toward removing the barriers to exploring new SLIM tracks and the likelihood of layout errors that require considerable revision and engineering time, the SLIM Pickins and pigsim tools (included as Supporting Information) allow the user to quickly design a length of planar ion guide, simulate its abilities to confine and transmit ions, compare hypothetical board outlines to given vacuum chamber dimensions, and generate a near-production ready PCB CAD file. In addition to these tools, this report outlines a series of cost-saving strategies with respect to vacuum feedthroughs and vacuum chamber design for TW ion mobility experiments using planar ion guides

Direct Real-Time Detection of RDX Vapors Under Ambient Conditions

The results in this manuscript represent a demonstration of RDX vapor detection in real time at ambient temperature without sample preconcentration. The detection of vapors from the low volatility explosive compound RDX was achieved through selective atmospheric pressure chemical ionization using nitrate reactant ions (NO₃^–) and NO₃^–·HNO₃ adducts generated in an electrical discharge source. The RDX vapors were ionized in a reaction region, which provided a variable (up to several seconds) reaction time. The reaction times were controlled either by flow in an atmospheric flow tube (AFT) or by an electric field in an atmospheric drift tube (ADT). Both AFT and ADT were interfaced to a quadrupole mass spectrometer for ion detection and identification. Recorded signals were observed for RDX concentrations below 25 ppq using selected ion monitoring (SIM) of the RDX-nitrate adduct at <i>m</i>/<i>z</i> 284

Development of Untargeted Metabolomics Methods for the Rapid Detection of Pathogenic <i>Naegleria fowleri</i>

Despite comparatively low levels of infection, primary amoebic meningoencephalitis (PAM) induced by <i>Naegleria fowleri</i> is extremely lethal, with mortality rates above 95%. As a thermophile, this organism is often found in moderate-to-warm climates and has the potential to colonize drinking water distribution systems (DWDSs). Current detection approaches require days to obtain results, whereas swift corrective action can maximize the benefit of public health. Presently, there is little information regarding the underlying in situ metabolism for this amoeba but the potential exists to exploit differentially expressed metabolic signatures as a rapid detection technique. This research outlines the biochemical profiles of selected pathogenic and nonpathogenic <i>Naegleria</i> in vitro using an untargeted metabolomics approach to identify a panel of diagnostically meaningful compounds that may enable rapid detection of viable pathogenic <i>N. fowleri</i> and augment results from traditional monitoring approaches

Improving Ion Mobility Mass Spectrometry of Proteins through Tristate Gating and Optimization of Multiplexing Parameters

Coupling drift tube ion mobility (IM) to Fourier transform mass spectrometry (FT-MS) affords the opportunity for gas-phase separation of ions based on size and conformation with high-resolution mass analysis. However, combining IM and FT-MS is challenging because ions exit the drift tube on a much faster time scale than the rate of mass analysis. Fourier transform (FT) and Hadamard transform multiplexing methods have been implemented to overcome the duty-cycle mismatch, offering new avenues for obtaining high-resolution, high-mass-accuracy analysis of mobility-selected ions. The gating methods used to integrate the drift tube with the FT mass analyzer discriminate against the transmission of large, low-mobility ions owing to the well-known gate depletion effect. Tristate gating strategies have been shown to increase ion transmission for drift tube IM-FT-MS systems through implementation of dual ion gating, controlling the quantity and timing of ions through the drift tube to reduce losses of slow-moving ions. Here we present an optimized set of multiplexing parameters for tristate gating ion mobility of several proteins on an Orbitrap mass spectrometer and further report parameters for increased ion transmission and mobility resolution as well as decreased experimental times from 15 min down to 30 s. On average, peak intensities in the arrival time distributions (ATDs) for ubiquitin increased 2.1× on average, while those of myoglobin increased by 1.5× with a resolving power increase on average of 11%

Tuning Mobility Separation Factors of Chemical Warfare Agent Degradation Products via Selective Ion-Neutral Clustering

Combining experimental data with computational modeling, we illustrate the capacity of selective gas-phase interactions using neutral gas vapors to yield an additional dimension of gas-phase ion mobility separation. Not only are the mobility shifts as a function of neutral gas vapor concentration reproducible, but also the selective alteration of mobility separation factors is closely linked to existing chemical functional groups. Such information may prove advantageous in elucidating chemical class and resolving interferences. Using a set of chemical warfare agent simulants with nominally the same reduced mobility values as a test case, we illustrate the ability of the drift-gas doping approach to achieve separation of these analytes. In nitrogen, protonated forms of dimethyl methyl phosphonate (DMMP) and methyl phosphonic acid (MPA) exhibit the reduced mobility values of 1.99 ± 0.01 cm² V^–1s^–1 at 175 °C. However, when the counter current drift gas of the system is doped with 2-propanol at 20 μL/h, full baseline resolution of the two species is possible. By varying the concentration of the neutral modifier, the separation factor of the respective clusters can be adjusted. For the two species examined and at a 2-propanol flow rate of 160 μL/h, MPA demonstrated the greatest shift in mobility (1.58 cm²V^–1s^–1) compared the DMMP monomer (1.63 cm²V^–1s^–1). Meanwhile, the DMMP dimer experienced no change in mobility (1.45 cm²V^–1s^–1). The enhancement of separation factors appears to be brought about by the differential clustering of neutral modifiers onto different ions and can be explained by a model which considers the transient binding of a single 2-propanol molecule during mobility measurements. Furthermore, the application of the binding models not only provides a thermodynamic foundation for the results obtained but also creates a predictive tool toward a quantitative approach

Atmospheric Pressure Drift Tube Ion Mobility–Orbitrap Mass Spectrometry: Initial Performance Characterization

Atmospheric pressure drift tube ion mobility spectrometry (AP-DTIMS) was coupled with Fourier transform Orbitrap mass spectrometry. The performance capabilities of this versatile new arrangement were demonstrated for different DTIMS ion gating operation modes and Orbitrap mass spectrometer parameters with regard to sensitivity and resolving power. Showcasing the optimized AP-DTIMS-Orbitrap MS system, isobaric peptide and sugar isomers were successfully resolved and the identities of separated species validated by high-energy collision dissociation experiments

Ambient Pressure Inverse Ion Mobility Spectrometry Coupled to Mass Spectrometry

Although higher resolving powers are often achieved using ambient pressure drift tube ion mobility mass spectrometry (DT-IMMS) systems, lower duty cycles are often required which directly impacts sensitivity. Moreover, the mechanism of ion gating using Bradbury-Nielsen or Tyndall-Gate configurations routinely results in ion gate depletion effects which discriminate against low mobility ions. This paper reports a new method of ambient pressure ion mobility operation in which inverse ion mobility spectrometry is coupled to a time-of-flight mass spectrometer to improve sensitivity and minimize the effects of ion gate depletion. In this mode of operation, the duty cycle is improved to approximate 99% from a typical value of less than 1%, improving the signal intensity by over 2 orders of magnitude. Another advantage of inverse ion mobility mass spectrometry is a reduction of the impact of ion gate depletion on low mobility molecules that translates into higher sensitivity for this class of analytes. To demonstrate these benefits afforded by this instrumental mode of operation differences in sensitivity, resolving power, and ion discrimination are compared between the inverse and normal modes of operation using tetraalkylammonium standards. These results show that the ion throughput is significantly increased for analytes with a broad range of mobilities with little impact on resolving power. While the mobility-based discrimination is minimized using the inverse mode of operation, the noise level in the inverse mode is highly dependent upon the stability of ionization source

Noticiero de Vigo : diario independiente de la mañana: Ano XXII Número 9648 - 1906 setembro 3

Here we demonstrate that when <i>Yersinia pesitis</i> is grown in laboratory media, peptides from the medium remain associated with cellular biomass even after washing and inactivation of the bacteria by different methods. These peptides are characteristic of the type of growth medium and of the manufacturer of the medium, reflecting the specific composition of the medium. We analyzed biomass-associated peptides from cultures of two attenuated strains of <i>Yersinia pestis</i> [KIM D27 (<i>pgm-</i>) and KIM D1 (<i>lcr-</i>)] grown in several formulations of 4 different media (tryptic soy broth (TSB), brain–heart infusion (BHI), Luria–Bertani broth (LB), and glucose (G) medium) made from components purchased from different suppliers. Despite the range of growth medium sources and the associated manufacturing processes used in their production, a high degree of peptide similarity was observed for a given medium recipe; however, notable differences in the termination points of select peptides were observed in media formulated using products from some suppliers, presumably reflecting the process by which a manufacturer performed protein hydrolysis for use in culture media. These results may help explain the presence of peptides not explicitly associated with target organisms during proteomic analysis of microbes and other biological systems that require culturing. While the primary aim of this work is to outline the range and type of medium peptides associated with <i>Yersinia pestis</i> biomass and improve the quality of proteomic measurements, these peptides may also represent a potentially useful forensic signature that could provide information about microbial culturing conditions

Second-Generation Tunable pH-Sensitive Phosphoramidate-Based Linkers for Controlled Release

We developed a second generation of tunable pH-sensitive linkers based on our phosphoramidate scaffold to release amine-containing drugs under acidic conditions. The pH-triggered phosphoramidate-based linkers are responsive to pH and do not require intracellular enzymatic action to initiate drug release. On the basis of the model scaffolds examined, phosphoramidate-based linkers were selected for particular properties for controlled release applications such as amine type, stability under physiological conditions, or release rates at various pH values such as intracellular endosomal conditions. Key to the pH-triggered amine release from these linker is a proximal carboxylic acid to promote hydrolysis of the phosphoramidate P–N bond, presumably through an intramolecular general acid-type mechanism. Phosphoramidate hydrolysis is largely governed by the p<i>K</i>_a of the leaving amine. However, the proximity of the neighboring carboxylic acid attenuates the stability of the P–N bond to hydrolysis, thus allowing for control over the release of an amine from the phosphoramidate center. In addition, we observed that the Thorpe–Ingold effect and rigidification of the scaffold could further enhance the rate of release. Esterification of the neighboring carboxylic acid was found to protect the scaffold from rapid release at low pH. This latter observation is particularly noteworthy as it suggests that the phosphoramidate-based drug–conjugate scaffold can be protected as an ester prodrug for oral administration. While the tunability phosphoramidate linkers is attractive for applications in intracellular trafficking studies in which pH changes can trigger release of turn-on dyes, antibody drug conjugates, small-molecule drug conjugates, and drug eluting stents (DES), the promise of oral delivery of drug conjugates is expected to have broad impact in controlled release applications