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Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions
The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50,000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire dataset. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property—the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good tradeoff between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.
Characterization of uncertainties in electron-argon collision cross sections
Abstract The predictive capability of a plasma discharge model depends on accurate representations of electron-impact collision cross sections, which determine the corresponding reaction rates and electron transport properties. The values of cross sections can be known only approximately either through experiments or simulations and are thus subject to uncertainties. Quantifying the uncertainties in plasma simulations allows us to assess the reliability of simulations and to provide a basis for interpreting discrepancies between simulations and experiments. For such uncertainty quantification of plasma simulations, it is essential to quantify the uncertainties of the underlying cross sections. Although much effort has been committed to calibrate the cross section values, their uncertainties are not well investigated. We characterize uncertainties in electron-argon atom collision cross sections using a Bayesian framework. Six collision processes—elastic momentum transfer, ionization, and four excitations—are characterized with semi-empirical models, which effectively capture the features important to the macroscopic properties of the plasma. A probability model for the uncertain parameters of these semi-empirical models is developed. Specifically, a Gaussian-process likelihood model is proposed to capture discrepancies among data sets, as well as the model-form inadequacies of the semi-empirical models. Two other likelihood models are compared with the proposed Gaussian-process model, to illustrate the importance of the choice of the likelihood model. The cross section models are calibrated using the electron-beam experiments and ab-inito quantum simulations. The resulting calibrated uncertainties capture well the scattering among the data sets. The calibrated cross section models are further validated against swarm-parameter experiments and zero-dimensional Boltzmann equation simulations of widely used cross section datasets.
Assessing Collision Cross Section Calibration Strategies for Traveling Wave-Based Ion Mobility Separations in Structures for Lossless Ion Manipulations
The collision cross section (CCS) is an important property that aids in the structural characterization of molecules. Here, we investigated the CCS calibration accuracy with traveling waves ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM) using three sets of calibrants. A series of singly negatively-charged phospholipids and bile acids were calibrated in nitrogen buffer gas using two different TW waveform profiles (square and sine) and amplitudes (20 V0-p, 25 V0-p, and 30 V 0-p ). The calibration errors for the three calibrant sets Agilent tuning mixture and polyalanine, and one assembled in-house showed negligible differences using a sine-shaped TW waveform. Furthermore, calibration errors were all within 1-2 % of the DTIMS measurements, with lower errors for sine waveforms, presumably due to the lower average and maximum fields experienced by ions. Finally, ultrahigh resolution multi-pass (long path length) SLIM TWIMS demonstrated improved CCS calibration for phospholipid and bile acid isomers.
Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-Based High-Resolution Ion Mobility Spectrometry–Mass Spectrometry
Ion mobility spectrometry (IMS) is a gas-phase analytical technique that separates ions with different sizes and shapes and is compatible with mass spectrometry (MS) to provide an additional separation dimension. The rapid nature of the IMS separation combined with the high sensitivity of MS-based detection and the ability to derive structural information on analytes in the form of the property collision cross section (CCS) makes IMS particularly well-suited for characterizing complex samples in -omics applications. In such applications, the quality of CCS from IMS measurements is critical to confident annotation of the detected components in the complex -omics samples. However, most IMS instrumentation in mainstream use requires calibration to calculate CCS from measured arrival times, with the most notable exception being drift tube IMS measurements using multifield methods. The strategy for calibrating CCS values, particularly selection of appropriate calibrants, has important implications for CCS accuracy, reproducibility, and transferability between laboratories. The conventional approach to CCS calibration involves explicitly defining calibrants ahead of data acquisition and crucially relies upon availability of reference CCS values. In this work, we present a novel reference-free approach to CCS calibration which leverages trends among putatively identified features and computational CCS prediction to conduct calibrations post-data acquisition and without relying on explicitly defined calibrants. We demonstrated the utility of this reference-free CCS calibration strategy for proteomics application using high-resolution structures for lossless ion manipulations (SLIM)-based IMS-MS. In conclusion, we first validated the accuracy of CCS values using a set of synthetic peptides and then demonstrated using a complex peptide sample from cell lysate.
PubChemLite Plus Collision Cross Section (CCS) Values for Enhanced Interpretation of Nontarget Environmental Data
Finding relevant chemicals in the vast (known) chemical space is a major challenge for environmental and exposomics studies leveraging nontarget high resolution mass spectrometry (NT-HRMS) methods. Chemical databases now contain hundreds of millions of chemicals, yet many are not relevant. This article details an extensive collaborative, open science effort to provide a dynamic collection of chemicals for environmental, metabolomics, and exposomics research, along with supporting information about their relevance to assist researchers in the interpretation of candidate hits. The PubChemLite for Exposomics collection is compiled from ten annotation categories within PubChem, enhanced with patent, literature and annotation counts, predicted partition coefficient (logP) values, as well as predicted collision cross section (CCS) values using CCSbase. Monthly versions are archived on Zenodo under a CC-BY license, supporting reproducible research, and a new interface has been developed, including historical trends of patent and literature data, for researchers to browse the collection. This article details how PubChemLite can support researchers in environmental and exposomics studies, describes efforts to increase the availability of experimental CCS values, and explores known limitations and potential for future developments. The data and code behind these efforts are openly available.
A Quantum Mechanical Treatment of Electron Broadening in Strong Magnetic Fields. II. Large Enhancements due to Exchange Interactions
We present a quantum treatment of atom–electron collisions in magnetic fields, demonstrating the significant importance of including the effect of exchange that arises from two interacting electrons. We find strange behaviors that are not encountered in collisions without a magnetic field. In high magnetic fields, exchange can lead to orders of magnitude enhancements of collision cross sections. Additionally, the elastic collision cross sections that involve the ground state become comparable to those involving excited states, and states with large orbits have the largest contribution to the collisions. We anticipate significant changes to spectral line broadening in neutron star surfaces and atmospheres.
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry
Abstract Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).
Agilent CRADA (Abstract)
The CRADA between Agilent Technologies Inc. and Battelle will focus on five software components as listed below: Prototype 4D Feature Finding functionality with a particular focus on recovering low level features and extending the bottom end dynamic range of IM-MS technology. Compare and contrast developments to current 4D Feature Finding capabilities. Highlight important algorithmic aspects employed. Implement the PNNL saturation correction algorithm. Agilent will give PNNL the needed data file access API and assistance in understanding it implementation and any needed instrumental aspects. Supported high resolution products to include Agilent’s TOF, QTOF and IM-QTOF mass spectrometers. PNNL will then work with Agilent to benchmark performance. Implementation of the PNNL Hadamard de-multiplexing algorithm. Agilent will give provide PNNL the needed date file access API access and as needed assistance in understanding the current Agilent multiplexed IM offering. PNNL will then work with Agilent on benchmark performance. Add ion mobility collision cross sections to existing and new metabolomic libraries for data analysis with Agilent’s informatics program MPP/ID Browser. PNNL will work with Agilent to create a software pipeline that takes data from chemical and metabolic standards and properly formats it for inclusion in MPP accessible libraries, using the collision cross section as a new separation dimension. Improvements of MPP multidimensional matching to identify metabolomic features using multiple characteristics beyond retention time and accurate mass. Most significantly matching will include analyte collision cross section with proposed support for sample fraction or RapidFire cartridge and fragmentation spectra. PNNL will work with Agilent to modify and improve the current MPP analysis pipeline to allow for creating, aligning, and identifying MS features defined by accurate mass, collision cross section and chromatographic retention time. As additional criteria such as fraction or RapidFire cartridge type are supported in the identification process, then they also will become part of the automation workflow. This includes the automation of said system to work with command line program (i.e. not a GUI) sufficient for programmatic execution in a pipeline.
Measurement of the Z(-> l(+)l(-))gamma production cross-section in pp collisions at root s=13 TeV with the ATLAS detector
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Collaborative Research: Unravelling the Physics Associated with the Production of Extremely Dense Plasma States of Microscale (Final Report) Nanosecond-pulsed Discharges
The aim of this project is to study and establish the physical mechanisms that contribute to the formation of anomalously dense plasmas in high-pressure nanosecond-pulsed discharges. These discharges have a broad range of applications such as plasma-assisted combustion, plasma flow actuators, biomedical sterilization and exotic materials synthesis. The structure and formation of these discharges, producing high plasma densities of ~10 14 -10 15 cm -3 , are well-studied and understood. Fast-pulsed microscale high-pressure discharges can be driven to even higher densities of > 10 19 cm -3 , approaching warm dense matter conditions. The mechanisms that generate these plasmas have not been understood. Analysis of the warm dense matter state under laboratory conditions is an expensive and non-trivial endeavor. For instance, dense plasmas can be generated by electrical explosions of metal foils and wires. Plasmas generated after the explosion have a short lifetime and often present difficult conditions for diagnostics. Generation of dense plasmas was also achieved during high-voltage nanosecond pulsed discharges when the so-called explosive electron emission is obtained. Unfortunately, this process is very difficult to control for the studies of warm dense matter. In our recent study, we have shown that additional heating of plasma by lasers can further increase the density of plasma and even lead to the fully ionized state. This method, potentially, allows better control of the plasma parameters. In this work, we studied a second stage laser-heated micro-discharge using a self-consistent one-dimensional particle-in-cell Monte Carlo-collision (1D PIC-MCC) model coupled with Maxwell’s equations. We predicted the generation of a fully ionized plasma on the picosecond time scale. However, this model considered the plasma as an ideal gas despite the high pressure and the nearly fully ionized state. The ideal plasma model assumes that the dilute gas approximation is valid, where the inter-particle interactions are negligible. For charged particles this assumption holds as long as the shielded Coulomb potential assumption is valid. For very high plasma densities, this concept breaks down since the Debye sphere surrounding each charged particle no longer contains enough electrons to statistically provide the shielding of the single particle Coulomb interaction potential. At such densities, the plasma can no longer be described as ideal and non-ideal coupling effects need to be considered. In this report, we elucidate our recent work of developing a PIC-MCC model with improvements for non-ideal plasma conditions due to Coulomb coupling at high densities. In particular, we study the interaction of green light radiation and a dense microplasma, and explore the non-ideal plasma effects in this interaction. In this computational model, we implement the two most important non-ideal effects: ionization potential depression (IPD) and enhanced collision cross sections. Our primary goal is to study the physics associated with electromagnetic (EM) wave heating, also called the second-stage wave-heating, and establish the role of plasma non-ideality in this phenomenon. Our secondary goal is to improve the chemistry mechanism of the 1D PIC-MCC model by including a more detailed excited species collision treatment. At high pressures, stepwise ionization from excited species might play an important role in the ionization process. Previously, this ionization mechanism was neglected due to the excitation collision cross section of xenon being smaller than that of ionization. However, a preliminary study showed that the excited species density in the initial microplasma was an order of magnitude higher than the electron density. Therefore, my aim is to determine the significance of this additional ionization pathway to the plasma generation.
Effects of screening and pressure ionization on the electron broadening of spectral lines in dense plasmas
Collisions between electrons and radiating atoms broaden spectral absorption and emission lines in dense plasmas. High densities also introduce screening and pressure ionization effects that distort the wave functions of both bound and free electrons. In order to study how dense plasma effects influence the electron broadening of spectral lines, this paper incorporates electron wave functions from an average-atom (AA) model to calculate the linewidth of the B III 2𝑝−2𝑠 transition at 𝑇 = 10 eV for mass densities ranging from 𝜌 = 10 −4 to 0.4 g/cc. The calculation method uses the impact approximation, allowing the linewidth to be written in terms of electron-collision cross sections and an interference term. Compared to an otherwise identical calculation that uses Coulomb free wave functions, the AA method is found to modify both the cross sections and the resulting linewidth at sufficiently high density by introducing screening and pressure-ionized bound states. Screening lowers the cross sections at low energies and near electron excitation thresholds, while pressure-ionized bound states introduce resonances into the continuum. Thus, as the density increases, the relative linewidth between the AA and Coulomb calculations follows a general decrease because of screening, with sharp increases at various intervals due to pressure ionization. Finally, the AA results are also compared with a common approach to introduce screening through the interaction potential and reduced models that use the Bethe formula for the inelastic electron-collision cross sections.
Measurement of inclusive 𝐽/𝜓 pair production cross section in 𝑝𝑝 collisions at √𝑠=13 TeV
The production cross section of inclusive J/ψ pairs in pp collisions at a center-of-mass energy $\sqrt{s}$ = 13 TeV is measured with ALICE. The measurement is performed for J/ψ in the rapidity interval 2.5 < y < 4.0 and for transverse momentum p T > 0. The production cross section of inclusive J/ψ pairs is reported to be 10.3 ±2.3(stat.) ±1.3(syst.) nb in this kinematic interval. The contribution from nonprompt J/ψ (i.e., originated from beauty-hadron decays) to the inclusive sample is evaluated. The effective double-parton scattering cross section is computed, neglecting the single-parton scattering contribution.
Measurement of the Υ(1S), Υ(2S), and Υ(3S) differential cross sections in pp collisions at $\sqrt{s}=13.6$ TeV
The production cross sections of the Υ(1S), Υ(2S), and Υ(3S) mesons are measured in proton-proton collisions at $\sqrt{s}=13.6$ TeV, using a data sample collected in 2022 by the CMS experiment and corresponding to an integrated luminosity of 37.4 fb −1 . The measurement is performed in the μ + μ − decay channels, differentially as a function of transverse momentum in the 20–200 GeV range, in the |y| < 0.6 and 0.6 < |y| < 1.2 rapidity intervals.
Measurement of $J/ψ$ production cross-sections in $pp$ collisions at $\sqrt{s}$ = 5 TeV
The production cross-sections of J/ψ mesons in proton-proton collisions at a centre-of-mass energy of $\sqrt{s} = 5 TeV are measured using a data sample corresponding to an integrated luminosity of 9.13 ± 0.18 pb -1 , collected by the LHCb experiment. The cross-sections are measured differentially as a function of transverse momentum, p T , and rapidity, y, and separately for J/ψ mesons produced promptly and from beauty hadron decays (nonprompt). With the assumption of unpolarised J/ψ mesons, the production cross-sections integrated over the kinematic range 0 < p T < 20 GeV/c and 2.0 < y < 4.5 are σ prompt J/Ψ = 8.154 ± 0.010 ± 0.283 μb, σnonprompt J/Ψ = 0.820 ± 0.003 ± 0.034 μb, where the first uncertainties are statistical and the second systematic. These cross-sections are compared with those at $\sqrt{s}$ = 8 TeV and 13 TeV, and are used to update the measurement of the nuclear modification factor in proton-lead collisions for J/ψ mesons at a centre-of-mass energy per nucleon pair of $\sqrt{s_{NN}}$ = 5 TeV. The results are compared with theoretical predictions.
Measurement of the top quark pair production cross section in PbPb collisions at $\sqrt{s_{\mathrm{NN}}}=5.36$ TeV
The inclusive cross section for top quark pair ($\mathrm{t}\overline{\mathrm{t}}$) production in lead-lead (PbPb) collisions is reported for the first time at a center-of-mass energy per nucleon pair of 5.36 TeV. The analysis uses data corresponding to an integrated luminosity of 1.58 nb −1 collected by the CMS experiment at the CERN LHC in 2023. The $\mathrm{t}\overline{\mathrm{t}}$ production cross section, ${\sigma}_{\mathrm{t}\overline{\mathrm{t}}}={3.42}_{-0.51}^{+0.54}{\left(\mathrm{stat}\right)}_{-0.43}^{+0.50}\left(\mathrm{syst}\right)$ μb, is measured in dilepton final states using a fit to a multivariate discriminator that combines the decay electron and muon kinematic properties with the multiplicity of bottom quark jets. The result is consistent with perturbative quantum chromodynamics calculations at next-to-next-to-leading order (NNLO) accuracy employing several nuclear parton distribution functions. In addition, the Drell–Yan production cross section (σ DY ) for dilepton masses above 10 GeV and the ratio of $\mathrm{t}\overline{\mathrm{t}}$ to DY cross sections $\left({R}_{\mathrm{t}\overline{\mathrm{t}}/\mathrm{DY}}\right)$ are found to be compatible with the NNLO predictions. The observables ${\sigma}_{\mathrm{t}\overline{\mathrm{t}}}$, σ DY , and ${R}_{\mathrm{t}\overline{\mathrm{t}}/\mathrm{DY}}$ are measured separately for central and semicentral PbPb collisions to investigate for the first time the dependence of top quark production on the collision impact parameter.
Measurement of the inclusive WZ production cross section in pp collisions at $\sqrt{\textrm{s}}$ = 13.6 TeV
The inclusive WZ production cross section is measured in proton-proton collisions at a centre-of-mass energy of 13.6 TeV, using data collected during 2022 with the CMS detector, corresponding to an integrated luminosity of 34.7 fb −1 . The measurement uses multileptonic final states and a simultaneous likelihood fit to the number of events in four different lepton flavour categories: eee, ee μ , μμ e, and μμμ . The selection is optimized to minimize the number of background events, and relies on an efficient prompt lepton discrimination strategy. The WZ production cross section is measured in a phase space defined within a 30 GeV window around the Z boson mass, as σ total (pp → WZ) = 55.2 ± 1.2 (stat) ± 1.2 (syst) ± 0.8 (lumi) ± 0.3 (theo) pb. In addition, the cross section is measured in a fiducial phase space closer to the detector-level requirements. All the measurements presented in this paper are in agreement with standard model predictions.
Measurement of the inclusive isolated-photon production cross section in pp collisions at $\mathbf {\sqrt{\textit{s}}=13}$ TeV
The production cross section of inclusive isolated photons has been measured by the ALICE experiment at the CERN LHC in pp collisions at centre-of-momentum energy of $\mathbf {\sqrt{\textit{s}}=13}$ TeV collected during the LHC Run 2 data-taking period. The measurement is performed by combining the measurements of the electromagnetic calorimeter EMCal and the central tracking detectors ITS and TPC, covering a pseudorapidity range of and a transverse momentum range of |η γ | < 0.67 and a transverse momentum range 7 < p$^{γ}_{T}$ < 200 GeV/c. The result extends to lower p$^{γ}_{T}$ and x$^{γ}_{T}$ = 2p$^{γ}_{T}$/$\sqrt{s}$ ranges, the lowest x$^{γ}_{T}$ of any isolated photon measurements to date, extending significantly those measured by the ATLAS and CMS experiments towards lower p$^{γ}_{T}$ at the same collision energy with a small overlap between the measurements. The measurement is compared with next-to-leading order perturbative QCD calculations and the results from the ATLAS and CMS experiments as well as with measurements at other collision energies. The measurement and theory prediction are in agreement with each other within the experimental and theoretical uncertainties.