Collision Cross Sections Research Articles

Elastic cross section data for precursor molecules used in low-temperature plasmas: Sn(CH3)4 and Ga(CH3)3

Tetramethyltin [Sn(CH3)4] and trimethylgallium [Ga(CH3)3] are important source molecules of Sn and Ga atoms which are used in manufacturing techniques involving low-temperature plasmas. Accurate numerical modeling of plasma environments requires a comprehensive set of electron scattering cross sections by these precursor molecules. Here, we report the elastic integral, differential, and momentum transfer cross sections for electron collisions with Sn(CH3)4 and Ga(CH3)3 for energies ranging from 0 to 30 eV. Our calculations were carried out with the Schwinger multichannel method implemented with pseudopotentials and considered two levels of approximation in our calculations, namely static-exchange and static-exchange plus polarization. We identified three shape resonances for Sn(CH3)4 and one clear low-lying resonance for Ga(CH3)3. The low-energy behavior of the s-wave cross section and eigenphase was investigated and, for both molecules, we found evidence of a Ramsauer–Townsend (RT) minimum and a virtual state. Our results indicate that negative differential conductivity would occur in a gas composed of Sn(CH3)4. On the other hand, this effect would be suppressed in a gas of Ga(CH3)3 due to an overlap between the position of the RT minimum and the shape resonance in the momentum-transfer cross section.

Cyclic Ion Mobility of Isomeric New Psychoactive Substances Employing Characteristic Arrival Time Distribution Profiles and Adduct Separation.

Analysis of new psychoactive substances (NPS), which is essential for toxicological and forensic reasons, can be made complicated by the presence of isomers. Ion mobility has been used as a standalone technique or coupled to mass spectrometry to detect and identify NPS. However, isomer separation has so far chiefly relied on chromatography. Here we report on the determination of isomeric ratios using cyclic ion mobility-mass spectrometry without any chromatographic separation. Isomers were distinguished by mobility separation of lithium adducts. Alternatively, we used arrival time distribution (ATD) profiles that were characteristic of individual isomers and were acquired for protonated molecules or fragment ions. Both approaches provided comparable results. Calculations were used to determine the structures and collision cross sections of both protonated and lithiated isomers that accurately characterized their ion mobility properties. The applicability of ATD profiles to isomer differentiation was demonstrated using direct infusion and flow injection analysis with electrospray of solutions, as well as desorption electrospray of solid samples. Data processing was performed by applying multiple linear regression to the ATD profiles. Using the proposed ATD profile-based approach, the relationships between the determined and given content of isomers showed good linearity with coefficients of determination typically greater than 0.99. Flow injection analysis using an autosampler allowed us to rapidly determine isomeric ratios in a sample containing two isomeric pairs with a minor isomer of 10% (determined 9.3% of 3-MMC and 11.0% of 3-FMC in a mixture with buphedrone and 4-FMC). The proposed approach is not only useful for NPS, but also may be applicable to small isomeric molecules analyzed by ion mobility when complete separation of isomers is not achieved.

Electron–ion collision and polarization of X-ray fluorescence radiation under hot quantum plasma conditions

In the current article, the spectral properties and electron collision (total and magnetic) excitation cross sections of ions taking placed in quantum plasmas are investigated. These cross sections are further used to study the polarization and angular distribution characteristics of the de-excitation radiation X-ray spectra, which play an important role in basic theoretical research, the diagnosis of the plasma environment, and the design of optical devices. To do so, a distorted wave method within the relativistic Dirac–Coulomb atomic structure scheme is suggested. The effective interaction potential between electrons and particles in hot quantum plasmas in the method is determined using a quantum approach that incorporates the influence of effective plasma screening effects caused by collective plasma oscillations. This potential replaces the traditional Coulomb interaction potential and is used in solving the modified Dirac equation to obtain the bound and continuum electron wave functions. Higher-order relativistic effects, such as the Breit interaction and the dominant quantum electrodynamics corrections, are added to enhance the accuracy of the method. Detailed calculations for the relativistic atomic structure and collision excitation dynamics process are carried out, taking the highly stripped H-like O7+ ion of astrophysical importance as an illustrative example. Detailed investigations are also conducted on the variation of energies, collision cross sections, and fluorescence polarizations as functions of the plasma parameters. Our results suggest that the joint effects of shielding and plasma coupling lead the energies, cross sections and fluorescence polarizations decrease (compared with the isolated case). The angular distribution of the X-ray fluorescence emission shows large change, suggesting their sensitivity to these effects. This study not only offers a valuable approach to investigating the plasma shielding and plasmon coupling effects in quantum plasmas but also holds significant relevance for applications in controlled nuclear fusion, astrophysical plasmas and so on.

High-resolution ion mobility based on traveling wave structures for lossless ion manipulation resolves hidden lipid features

High-resolution ion mobility (resolving power > 200) coupled with mass spectrometry (MS) is a powerful analytical tool for resolving isobars and isomers in complex samples. High-resolution ion mobility is capable of discerning additional structurally distinct features, which are not observed with conventional resolving power ion mobility (IM, resolving power ~ 50) techniques such as traveling wave IM and drift tube ion mobility (DTIM). DTIM in particular is considered to be the “gold standard” IM technique since collision cross section (CCS) values are directly obtained through a first-principles relationship, whereas traveling wave IM techniques require an additional calibration strategy to determine accurate CCS values. In this study, we aim to evaluate the separation capabilities of a traveling wave ion mobility structures for lossless ion manipulation platform integrated with mass spectrometry analysis (SLIM IM-MS) for both lipid isomer standards and complex lipid samples. A cross-platform investigation of seven subclass-specific lipid extracts examined by both DTIM-MS and SLIM IM-MS showed additional features were observed for all lipid extracts when examined under high resolving power IM conditions, with the number of CCS-aligned features that resolve into additional peaks from DTIM-MS to SLIM IM-MS analysis varying between 5 and 50%, depending on the specific lipid sub-class investigated. Lipid CCS values are obtained from SLIM IM (TW(SLIM)CCS) through a two-step calibration procedure to align these measurements to within 2% average bias to reference values obtained via DTIM (DTCCS). A total of 225 lipid features from seven lipid extracts are subsequently identified in the high resolving power IM analysis by a combination of accurate mass-to-charge, CCS, retention time, and linear mobility-mass correlations to curate a high-resolution IM lipid structural atlas. These results emphasize the high isomeric complexity present in lipidomic samples and underscore the need for multiple analytical stages of separation operated at high resolution.Graphical abstract

Hyphenation of supercritical fluid chromatography and trapped ion mobility-mass spectrometry for quantitative lipidomics

BackgroundLipidomics studies require rapid separations with accurate and reliable quantification results to further elucidate the role of lipids in biological processes and their biological functions. Supercritical fluid chromatography (SFC), in particular, can provide this rapid and high-resolution separation. The combination with trapped ion mobility spectrometry (TIMS) has not yet been applied, although the post-ionization separation method in combination with liquid chromatography or imaging techniques has already proven itself in resolving isomeric and isobaric lipids and preventing false identifications. However, a multidimensional separation method should not only allow confident identification but also provide quantitative results to substantiate studies with absolute concentrations. ResultsA SFC method was developed and the hyphenation of SFC and TIMS was further explored towards the separation of different isobaric overlaps. Furthermore, lipid identification was performed using mass spectrometry (MS) and parallel accumulation serial fragmentation (PASEF) MS/MS experiments in addition to retention time and collision cross section (CCS). Quantification was further investigated with short TIMS ramps and performed based on the ion mobility signal of lipids, since TIMS increases the sensitivity by noise filtering. The final method was, as an exemplary study, applied to investigate the function of different ceramide synthases (CerS) in the nematode and model organism Caenorhabditis elegans (C. elegans). Loss of three known CerS hyl-1, hyl-2 and lagr-1 demonstrated different influences on and alterations in the sphingolipidome. SignificanceThis method describes for the first time the combination of SFC and TIMS-MS/MS, which enables a fast and sensitive quantification of lipids. The results of the application to C. elegans samples prove the functionality of the method and support research on the metabolism of sphingolipids in nematodes.

Analytical characterization of anthocyanins using trapped ion mobility spectrometry-quadrupole time-of-flight tandem mass spectrometry

Anthocyanin profiles of juices from blueberry (Vaccinium myrtillus L.) and different grape varieties (Vitis labrusca L. cv. Concord, Vitis vinifera L. cvs. Accent, Dunkelfelder, Dakapo, and GM 674–1) were characterized by ultra-high performance liquid chromatography (UHPLC) coupled to trapped ion mobility spectrometry-quadrupole time-of-flight tandem mass spectrometry (TIMS-QTOF-MS/MS). Ion mobility and collision cross section (CCS) values of over 50 structurally related anthocyanins based on delphinidin, cyanidin, petunidin, peonidin, and malvidin were determined. Relations between molecular mass, mobility values, and specific structural features were revealed. The mass-to-charge (m/z) ratio of the molecular ions (M+) was found to be the major factor influencing anthocyanin ion mobilities, but structural characteristics also contributed to their variability. We were able to differentiate positional and geometrical isomers and certain epimers by their respective mobility values. For instance, whereas 3-O-hexosides (i.e., 3-O-glucosides and 3-O-galactosides) were separated by TIMS, epimers of 3-O-pentosides assessed could not be distinguished.

Using ion mobility spectrometry to understand signal dilution during tandem mass spectrometry sequencing of digital polymers: Experimental evidence of intramolecular cyclization.

Optimizing the structure of digital polymers is an efficient strategy to ensure their tandem mass spectrometry (MS/MS) readability. In block-truncated poly(phosphodiester)s, homolysis of C-ON bonds in long chains permits the release of smaller blocks amenable to sequencing. Yet the dissociation behavior of diradical blocks was observed to strongly depend on their charge state. Polymers were ionized in negative mode electrospray and activated in-source so that blocks released as primary fragments can be investigated using ion mobility spectrometry (IMS) or sequenced in the post-IMS collision cell. Collision cross sections (CCS) were derived from arrival times using a calibration procedure developed for polyanions using the IMSCal software. A multistep protocol based on quantum methods and classical molecular dynamics was implemented for molecular modeling and calculation of theoretical CCS. Unlike their triply charged homologues, dissociation of diradical blocks at the 2- charge state produces additional fragments, with +1m/z shift for those holding the nitroxide α-termination and -1m/z for those containing the carbon-centered radical ω-end. These results suggest cyclization of these diradical species, followed by H• transfer on activated reopening of this cycle. This assumption was validated using IMS resolution of the cyclic/linear isomers and supported by molecular modeling. Combining IMS with molecular modeling provided new insights into how the charge state of digital blocks influences their dissociation. These results permit to define new guidelines to improve either ionization conditions or the structural design of these digital polymers for best MS/MS readability.

Investigating the B-meson production based on the color dipole transverse momentum representation in pp collisions at the LHC

In this work the B-mesons differential cross sections in pp collisions are evaluated considering the color dipole formalism in transverse momentum representation along with the unintegrated gluon distributions (UGDs). Analytical parametrizations for UGDs including hard scale QCD evolution and those based on parton saturation framework are compared. The theoretical predictions for the B-meson production in terms of the transverse momentum distribution cover the center-of-mass energy of the Large Hadron Collider and the rapidities available at its experiments. The results for different B-mesons are compared to the corresponding measurements reported by the ATLAS, CMS, and LHCb experiments. Predictions are also performed for the nuclear modification factor as a function of the meson transverse momentum.

Elucidating the Gas-Phase Behavior of Nitazene Analog Protomers Using Structures for Lossless Ion Manipulations Ion Mobility-Orbitrap Mass Spectrometry.

2-Benzylbenzimidazoles, or "nitazenes", are a class of novel synthetic opioids (NSOs) that are increasingly being detected alongside fentanyl analogs and other opioids in drug overdose cases. Nitazenes can be 20× more potent than fentanyl but are not routinely tested for during postmortem or clinical toxicology drug screens; thus, their prevalence in drug overdose cases may be under-reported. Traditional analytical workflows utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS) often require additional confirmation with authentic reference standards to identify a novel nitazene. However, additional analytical measurements with ion mobility spectrometry (IMS) may provide a path toward reference-free identification, which would greatly accelerate NSO identification rates in toxicology laboratories. Presented here are the first IMS and collision cross section (CCS) measurements on a set of fourteen nitazene analogs using a structures for lossless ion manipulations (SLIM)-orbitrap MS. All nitazenes exhibited two high intensity baseline-separated IMS distributions, which fentanyls and other drug and druglike compounds also exhibit. Incorporating water into the electrospray ionization (ESI) solution caused the intensities of the higher mobility IMS distributions to increase and the intensities of the lower mobility IMS distributions to decrease. Nitazenes lacking a nitro group at the R1 position exhibited the greatest shifts in signal intensities due to water. Furthermore, IMS-MS/MS experiments showed that the higher mobility IMS distributions of all nitazenes possessing a triethylamine group produced fragment ions with m/z 72, 100, and other low intensity fragments while the lower mobility IMS distributions only produced fragment ions with m/z 72 and 100. The IMS, solvent, and fragmentation studies provide experimental evidence that nitazenes potentially exhibit three gas-phase protomers. The cyclic IMS capability of SLIM was also employed to partially resolve four sets of structurally similar nitazene isomers (e.g., protonitazene/isotonitazene, butonitazene/isobutonitazene/secbutonitazene), showcasing the potential of using high-resolution IMS separations in MS-based workflows for reference-free identification of emerging nitazenes and other NSOs.

Prediction of a complete and self-consistent collision cross-section set of C5F10O by data-driven method

The lack of a complete and consistent set of electron–molecule collision cross sections for the new eco-friendly gas C5F10O hinders the study of its microscopic discharge mechanisms. In this paper, we first calculate the elastic collision and electronic excitation cross-sections of C5F10O based on R-matrix theory and estimate its total attachment cross-sections through pulsed Townsend measurement. By combining cross sections from other literature, we are able to compile an initial set of collision cross-sections for C5F10O. However, this initial set remains incomplete and requires refinement. Therefore, this work establishes a neutral network to solve the inverse swarm problem of deriving cross-sections from swarm parameters. The inversion model is trained using a substantial amount of collision cross-sections from the LXCat project. Using the model and the initial set for C5F10O, a complete and self-consistent collision cross-section set for the C5F10O gas is predicted for the first time, based on the measured electron swarm parameters of C5F10O/Ar mixtures. The proposed method is capable of predicting C5F10O’s unknown vibrational excitation cross-section without any prior knowledge, thus enhancing its completeness. The refined set can reproduce the electron swarm parameters within an acceptable range of uncertainty, thus verifying its self-consistency. The set will be made available in the LXCat database, which is expected to be significant for fundamental studies of its discharge mechanisms as well as applications of C5F10O.

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. 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.

Elucidation of Dithiol-yne Comb Polymer Architectures by Tandem Mass Spectrometry and Ion Mobility Techniques.

Polymers have a wide range of applications depending on their composition, size, and architecture. Varying any of these three characteristics can greatly impact the resulting chemical, physical, and mechanical properties. While many techniques are available to determine polymer composition and size, determining the exact polymer architecture is more challenging. Herein, tandem mass spectrometry (MS/MS) and ion mobility mass spectrometry (IM-MS) methods are utilized to derive crucial architectural information about dithiol-yne comb polymers. Based on their unique fragmentation products and IM drift times, dithiol-yne oligomers with distinct architectures were successfully differentiated and characterized. Additionally, experimental collision cross-sections (Ω) derived via IM-MS were compared to theoretically extracted Ω values from molecular dynamics simulated structures to deduce the architectural motif of these comb oligomers. Overall, this work demonstrates the benefits of combining various mass spectrometry techniques in order to gain a complete understanding of a complex polymer mixture.

Ultrafast, Selective, and Highly Sensitive Nonchromatographic Analysis of Fourteen Cannabinoids in Cannabis Extracts, Δ8-Tetrahydrocannabinol Synthetic Mixtures, and Edibles by Cyclic Ion Mobility Spectrometry-Mass Spectrometry.

The diversity of cannabinoid isomers and complexity of Cannabis products pose significant challenges for analytical methodologies. In this study, we developed a method to analyze 14 different cannabinoid isomers in diverse samples within milliseconds by leveraging the unique adduct-forming behavior of silver ions in advanced cyclic ion mobility spectrometry-mass spectrometry. The developed method achieved the separation of isomers from four groups of cannabinoids: Δ3-tetrahydrocannabinol (THC) (1), Δ8-THC (2), Δ9-THC (3), cannabidiol (CBD) (4), Δ8-iso-THC (5), and Δ(4)8-iso-THC (6) (all MW = 314); 9α-hydroxyhexahydrocannabinol (7), 9β-hydroxyhexahydrocannabinol (8), and 8-hydroxy-iso-THC (9) (all MW = 332); tetrahydrocannabinolic acid (THCA) (10) and cannabidiolic acid (CBDA) (11) (both MW = 358); Δ8-tetrahydrocannabivarin (THCV) (12), Δ8-iso-THCV (13), and Δ9-THCV (14) (all MW = 286). Moreover, experimental and theoretical traveling wave collision cross section values in nitrogen (TWCCSN2) of cannabinoid-Ag(I) species were obtained for the first time with an average error between experimental and theoretical values of 2.6%. Furthermore, a workflow for the identification of cannabinoid isomers in Cannabis and Cannabis-derived samples was established based on three identification steps (m/z and isotope pattern of Ag(I) adducts, TWCCSN2, and MS/MS fragments). Afterward, calibration curves of three major cannabinoids were established with a linear range of 1-250 ng·ml-1 for Δ8-THC (2) (R2 = 0.9999), 0.1-25 ng·ml-1 for Δ9-THC (3) (R2 = 0.9987), and 0.04-10 ng·ml-1 for CBD (4) (R2 = 0.9986) as well as very low limits of detection (0.008-0.2 ng·ml-1). Finally, relative quantification of Δ8-THC (2), Δ9-THC (3), and CBD (4) in eight complex acid-treated CBD mixtures was achieved without chromatographic separation. The results showed good correspondence (R2 = 0.999) with those obtained by gas chromatography-flame ionization detection/mass spectrometry.

Hyphenation of Liquid Chromatography and Trapped Ion Mobility - Mass Spectrometry for Characterization of Isomeric Phosphatidylethanolamines with Focus on N-Acylated Species.

In prior research, hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry (HILIC-MS/MS) has demonstrated applicability for characterizing regioisomers in lipidomics studies, including phosphatidylglycerols (PG) and bis(monoacyl)glycerophosphates (BMP). However, there are other lipid regioisomers, such as phosphatidylethanolamines (PE) and lyso-N-acyl-PE (LNAPE), that have not been studied as extensively. Therefore, hyphenated mass spectrometric methods are needed to investigate PE and LNAPE regioisomers individually. The asymmetric structure of LNAPE favors isomeric species, which can result in coelution and chimeric MS/MS spectra. One way to address the challenge of chimeric MS/MS spectra is through mobility-resolved fragmentation using trapped ion mobility spectrometry (TIMS). Therefore, we developed a multidimensional HILIC-TIMS-MS/MS approach for the structural characterization of isomeric phosphatidylethanolamines in both negative and positive ionization modes. The study revealed the complementary fragmentation pattern and ion mobility behavior of LNAPE in both ionization modes, which was confirmed by a self-synthesized LNAPE standard. With this knowledge, a distinction of regioisomeric PE and LNAPE was achieved in human plasma samples. Furthermore, regioisomeric LNAPE species containing at least one unsaturated fatty acid were noted to exhibit a change in collision cross-section in positive ionization mode, leading to a lipid characterization with respect to fatty acyl positional level. Similar mobility behavior was also observed for the biological LNAPE precursor N-acyl-PE (NAPE). Application of this approach to plasma and cereal samples demonstrated its effectiveness in regioisomeric LNAPE and NAPE species' elucidation.

Exploring the Conformational Landscape of Poly(l-lysine) Dendrimers Using Ion Mobility Mass Spectrometry.

Ion mobility mass spectrometry (IM-MS) measures the mass, size, and shape of ions in the same experiment, and structural information is provided via collision cross-section (CCS) values. The majority of commercially available IM-MS instrumentation relies on the use of CCS calibrants, and here, we present data from a family of poly(l-lysine) dendrimers and explore their suitability for this purpose. In order to test these compounds, we employed three different IM-MS platforms (Agilent 6560 IM-QToF, Waters Synapt G2, and a home-built variable temperature drift tube IM-MS) and used them to investigate six different generations of dendrimers in two buffer gases (helium and nitrogen). Each molecule gives a highly discrete CCS distribution suggestive of single conformers for each m/z value. The DTCCSN2 values of this series of molecules (molecular weight: 330-16,214 Da) range from 182 to 2941 Å2, which spans the CCS range that would be found by many synthetic molecules including supramolecular compounds and many biopolymers. The CCS values for each charge state were highly reproducible in day-to-day analysis on each instrument, although we found small variations in the absolute CCS values between instruments. The rigidity of each dendrimer was probed using collisionally activated and high-temperature IM-MS experiments, where no evidence for a significant CCS change ensued. Taken together, this data indicates that these polymers are candidates for CCS calibration and could also help to reconcile differences found in CCS measurements on different instrument geometries.

H2CO and CS in diffuse clouds: Excitation and abundance

Context. Diffuse interstellar clouds present an active chemistry despite their relatively low density and the ubiquitous presence of far-UV radiation. Aims. To provide constraints on the chemical processes responsible for the observed columns of organic species, we used the NOEMA interferometer to observe the sight line toward NRAO150 (B0355+508) in the 2 mm spectral window. Methods. We targeted the low excitation lines of ortho H2 CO (21,1–11,0) and para H2 CO (20,2–10,1) as well as the nearby transitions of CS (3–2) and c-C3H2 (31,2–22,1), (41,4–30,3), and (22,0–11,1). We combined these data with previous observations of the same sight line to determine the excitation conditions, column densities, and abundances relative to H2 in the different velocity components. We performed non-LTE radiative transfer calculations including collision cross sections with ortho and para H2 and with electrons. New collision cross sections with electrons were computed for ortho and para formaldehyde. Results. All targeted lines were detected. The c-C3H2 line profiles are very similar to those of HCO+ and CCH, while the CS absorption features are narrower and mostly concentrated in two main velocity components at VLSR = −17.2 and −10.4 km s−1. H2CO absorption lines present an intermediate pattern with absorption in all velocity components but larger opacities in the two main velocity components. The ortho-to-para ratios of H2CO and c-C3H2 are consistent with the statistical value of three. While the excitation temperature of all c-C3H2 velocity components is consistent with the Cosmic Microwave Background (CMB), the two strong components detected in CS show a clear excess over the CMB indicating that CS resides at higher densities than other species along this particular sightline, n(H2) ~ 2500 cm−3 while n(H2) < 500 cm−3 for the other velocity components. We detected faint absorption from o-H213CO and C34S allowing us to derive isotopic ratios: o-H2CO/o-H213CO = 61 ± 12 and C32S/C34S = 24 ± 6. The excitation of the 11,0−11,1 line of formaldehyde at 4.8 GHz is sensitive to the electron fraction and its excitation temperature is predicted to be lower than the CMB at low and moderate electron fractions (x(e) < 6 × 10−5), and to rise above the CMB at high electron fractions (x(e) > 10−4).

Predicting the Predicted: A Comparison of Machine Learning-Based Collision Cross-Section Prediction Models for Small Molecules.

The application of machine learning (ML) to -omics research is growing at an exponential rate owing to the increasing availability of large amounts of data for model training. Specifically, in metabolomics, ML has enabled the prediction of tandem mass spectrometry and retention time data. More recently, due to the advent of ion mobility, new ML models have been introduced for collision cross-section (CCS) prediction, but those have been trained with different and relatively small data sets covering a few thousands of small molecules, which hampers their systematic comparison. Here, we compared four existing ML-based CCS prediction models and their capacity to predict CCS values using the recently introduced METLIN-CCS data set. We also compared them with simple linear models and with ML models that used fingerprints as regressors. We analyzed the role of structural diversity of the data on which the ML models are trained with and explored the practical application of these models for metabolite annotation using CCS values. Results showed a limited capability of the existing models to achieve the necessary accuracy to be adopted for routine metabolomics analysis. We showed that for a particular molecule, this accuracy could only be improved when models were trained with a large number of structurally similar counterparts. Therefore, we suggest that current annotation capabilities will only be significantly altered with models trained with heterogeneous data sets composed of large homogeneous hubs of structurally similar molecules to those being predicted.

Simulations of the hydrogen and deuterium thermal and non-thermal escape at Mars at Spring Equinox

We present simulations of the thermal and nonthermal escape processes for H and D, under atomic, molecular and ion forms at Mars during spring equinox. These processes include Jeans escape, several photochemical reactions and the escape associated to the solar wind interaction with Mars. While the hydrogen escape is dominated by the atomic Jeans escape, we find that the deuterium escape is dominated by the photochemical atomic escape. Ions escape represent only 10% of the total escape for both species and is mostly due to charge exchange between neutral and solar wind protons. Including all the processes, we find a D/H fractionation factor (D/H escape ratio divided by the D/H atmospheric ratio) f = 0.04, with a main uncertainty associated to the elastic collisional cross sections needed to accurately derive the photochemical escape rate. Using this fractionation factor and considering a 30 m exchangeable reservoir of water, the average hydrogen escape rate needed to fractionate the Martian water from its primordial value to its current D/H value during the last 4.5 Gyr is ∼1.0 × 1028 s−1 which is larger than the current average escape rate (∼ 2 × 1026 s−1).

Four-dimensional lipidomics profiling in X-linked adrenoleukodystrophy using trapped ion mobility mass spectrometry

Lipids play pivotal roles in an extensive range of metabolic and physiological processes. In recent years, the convergence of trapped ion mobility spectrometry and MS has enabled 4D-lipidomics, a highly promising technology for comprehensive lipid analysis. 4D-lipidomics assesses lipid annotations across four distinct dimensions—retention time, collisional cross section, m/z (mass-to-charge ratio), and MS/MS spectra—providing a heightened level of confidence in lipid annotation. These advantages prove particularly valuable when investigating complex disorders involving lipid metabolism, such as adrenoleukodystrophy (ALD). ALD is characterized by the accumulation of very-long-chain fatty acids (VLCFAs) due to pathogenic variants in the ABCD1 gene. A comprehensive 4D-lipidomics strategy of ALD fibroblasts demonstrated significant elevations of various lipids from multiple classes. This indicates that the changes observed in ALD are not confined to a single lipid class and likely impacts a broad spectrum of lipid-mediated physiological processes. Our findings highlight the incorporation of mainly saturated and monounsaturated VLCFA variants into a range of lipid classes, encompassing phosphatidylcholines, triacylglycerols, and cholesterol esters. These include ultra-long-chain fatty acids with a length of up to thirty carbon atoms. Lipid species containing C26:0 and C26:1 were the most frequently detected VLCFA lipids in our study. Furthermore, we report a panel of 121 new candidate biomarkers in fibroblasts, exhibiting significant differentiation between controls and individuals with ALD. In summary, this study demonstrates the capabilities of a 4D-lipid profiling workflow in unraveling novel insights into the intricate lipid modifications associated with metabolic disorders like ALD.

Study of the Conformational Dynamics of Prolyl Oligopeptidase by Mass Spectrometry: Lessons Learned.

Ion mobility mass spectrometry (IM-MS) can be used to analyze native proteins according to their size and shape. By sampling individual molecules, it allows us to study mixtures of conformations, as long as they have different collision cross sections and maintain their native conformation after dehydration and vaporization in the mass spectrometer. Even though conformational heterogeneity of prolyl oligopeptidase has been demonstrated in solution, it is not detectable in IM-MS. Factors that affect the conformation in solution, binding of an active site ligand, the stabilizing Ser554Ala mutation, and acidification do not qualitatively affect the collision-induced unfolding pattern. However, measuring the protection of accessible cysteines upon ligand binding provides a principle for the development of MS-based ligand screening methods.