An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements

Comprehensive analysis of oxidized arachidonoyl-containing glycerophosphocholines using ion mobility spectrometry-mass spectrometry

The biological significance of oxidized arachidonoyl-containing glycerophosphocholines, exemplified by the oxidation products of 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (oxPAPC), in pathological processes is well-established. However, despite their widespread use in redox lipidomics research, the precise chemical composition of the heterogeneous mixtures of oxPAPC generated in vitro -including the high prevalence of isomers and the oxidation mechanisms involved- remain inadequately understood. To address these knowledge gaps, we developed a multidimensional in-house database from a commercial oxPAPC preparation -employing Liquid Chromatography coupled to Quadrupole Time-of-Flight Mass Spectrometry (LC-QTOF-MS) and Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS). This database includes lipid names, retention times, accurate mass values (m/z), adduct profiles, MS/MS information, as well as collision cross-section (CCS) values. Our investigation elucidated 34 compounds belonging to distinct subsets of oxPAPC products, encompassing truncated, full-length, and cyclized variants. The integration of IMS-MS crucially facilitated: (i) structural insights among regioisomers, exemplified by the 5,6-PEIPC and 11,12-PEIPC epoxy-isoprostane derivatives, (ii) novel Collision Cross Section (CCS) values, and (iii) cleaner MS/MS spectra for elucidating the fragmentation mechanisms involved to yield specific fragment ions. These diagnostic ions were employed to successfully characterize full-length isomers present in human plasma samples from patients with mucormycosis. This comprehensive oxPAPC characterization not only advances the understanding of lipid peroxidation products but also enhances analytical capabilities for in vitro-generated oxidized mixtures. The implementation of this robust database, containing multiple orthogonal (i.e., independent) pieces of information, will serve as a comprehensive resource for the field.

Coupling Capillary Electrophoresis With a Shifted Inlet Potential High-Resolution Ion Mobility Spectrometer

We present the coupling of capillary electrophoresis to a custom-built high-resolution ion mobility spectrometer (IMS). This system integrates a shifted inlet potential IMS configuration with a customised nanoflow ESI sheath interface. It enables the rapid analysis of quaternary ammonium compounds (QACs) and their impurities in real-world samples. It allowed the detection of six non-chromophoric compounds in about 3 min. The assignment of the IMS signals to compounds was supported by matching experimentally determined collision cross-section (CCS) values with predicted values. The system achieved a detection limit in the single-digit picogram range with IMS resolutions of over 80.

Miniaturized Supercritical Fluid Chromatography Coupled with Ion Mobility Spectrometry: A Chip-Based Platform for Rapid Chiral and Complex Mixture Analysis

This study presents the first coupling of miniaturized chip-based supercritical fluid chromatography (SFC) with ion mobility spectrometry (IMS) enabling rapid two-dimensional analysis of moderately polar compounds. For the first time, ionization and analyte transfer at the SFC-IMS interface are achieved solely through eluent decompression in conjunction with a shifted electric IMS inlet potential. This straightforward approach significantly reduces instrumentation complexity and size, promoting system compactness and robustness. The integration of chip-based SFC with IMS enables high-speed separations of complex samples, drastically reducing analysis time while utilizing a detector capable of delivering structural information at a rapid acquisition rate and low cost. Evaluation of the SFC-IMS system as demonstrated through the chiral separation of Tröger's base revealed exceptional repeatability and sensitivity. Short columns and high flow rates resulted in record-speed SFC-IMS analysis in just six seconds. The system was successfully used to analyze a complex mixture containing five isomers, including naloxone and 6-monoacetylmorphine, in just 30 s.

Optimization of Collagenase Proteomics for Improved Mass Spectrometry Imaging Peptide Identification

The extracellular matrix (ECM) is composed of a dynamically regulated collagenous scaffold that provides structure, conveys cellular and environmental communication, and contributes to disease progression. Collagen proteins derived from clinically archived formalin-fixed, paraffin-embedded (FFPE) tissues are analytically challenging due to dense post-translational modifications, high proline content, and insolubility. A recent advancement in ECM proteomics is the use of collagenase type III, an ECM-specific bacterial protease, to target native collagenous structures on-tissue for peptide imaging. The resulting collagenase-generated peptides have biochemical differences compared to tryptic peptides, creating analytical challenges in elucidating peptide sequence information. In this study, we characterize collagenase as a proteomic enzyme for ECM-targeted liquid chromatography trapped ion mobility spectrometry tandem mass spectrometry (LC-TIMS-MS/MS) and matrix-assisted laser/desorption ionization mass spectrometry imaging (MALDI-MSI) proteomic workflows. We then optimized collagenase-generated peptide sequencing for MALDI-MSI peptide identification from clinically archived FFPE tissue sections. Soluble rat tail collagen solution is used as a collagen standard to elucidate tryptic and collagenase cleavage sites within collagen. Proteomic readouts of FFPE tissue are compared across trypsin and collagenase digests to assess for ECM enrichment by collagenase in biologically complex samples. Optimized methods for MALDI-MSI peptide identification are comprehensively detailed from sample preparation to MS data acquisition and MS data analysis for reproducible implementation. On-tissue digestion followed by liquid surface extraction (LSE), inclusion of singly charged peptides during data acquisition, and implementation of nonspecific cleavage during database searching resulted in the most collagenase-generated peptide spectrum matches as well as MALDI-MSI peptide identifications. This research establishes parameters for the optimal identification of peptides from collagenase-directed ECM proteomic workflows for targeted spatial analysis of the ECM.

FluoroMatch IM: An Interactive Software for PFAS Analysis by Ion Mobility Spectrometry

Per- and polyfluoroalkyl substances (PFASs) are often present in complex mixtures at trace levels in environmental samples, posing difficulties for analytical chemists. Ion mobility offers highly replicable identifiers, enabling the use of community-based libraries for PFAS annotation in nontargeted analysis. Currently, limited software exists to leverage the capabilities of liquid chromatography ion mobility high-resolution mass spectrometry (LC-IM-HRMS) for nontargeted analysis. FluoroMatch IM is a free vendor-neutral open-source tool for rapid annotation of PFASs in LC-IM-HRMS datasets. Annotation algorithms include collision cross-section (CCS) matching, formula prediction, homologous series detection, mass defect filtering, and accurate mass matching with a database of 194 PFAS ions that can be continuously expanded by the community. Results from FluoroMatch IM were compared to a targeted approach with a laboratory-prepared mixture of 63 PFASs and real wastewater samples. A nontarget workflow incorporating FluoroMatch IM revealed additional likely PFASs (n = 16) while confirming most targeted annotations (11/12) in wastewater samples. Validation of the standard mix showed a low false negative rate of 5% and a 5% false positive rate for features included in the CCS library, with a 0% false positive rate for features assigned confident scores. This study demonstrates the promise of FluoroMatch IM for streamlining PFAS analysis workflows.

Evaluating Ion Mobility Data Acquisition, Calibration, and Processing for Small Molecules: A Cross-Platform Assessment of Drift Tube and Traveling Wave Methodologies

As ion mobility spectrometry (IMS) separations continue to be added to analytical workflows due to their power in environmental and biological sample analyses, harmonization and capability understanding between existing and newly released instruments are desperately needed. Developments in IMS platforms often exhibit focus on increasing resolving power (Rp) to better separate molecules of similar structure. While the additional separation capacity is advantageous, ensuring these developments coincide with appropriate data extraction and analysis methods is imperative to ensure routine adoption. Herein, we assess the performance of the MOBILion MOBIE in relation to a commercially available drift tube IMS-MS, the Agilent 6560, and evaluate feature extraction and analysis pipelines. Both instruments were operated using matched conditions when possible, and performance metrics of scan speed, Rp, limits of detection (LOD), and propensity for isomer separation via LC-IMS-MS were evaluated. Similar scan speeds pertaining to IMS-MS frame generation were noted for both platforms, and collision cross section (CCS) values for the MOBIE were generally within ≤ 1% difference from previously reported drift tube values. Both platforms were also able to generate quantitative data (comparable limits of detection) in experiments with perfluoroalkyl substances (PFAS) mixtures in a cell-based model (both medium and cell lysates), as demonstrated in Skyline with adjusted mobility filtering parameters. Higher Rp was, however, noted on the MOBIE in comparison to the 6560 (200-300 vs 45-60 CCS/ΔCCS without data processing), allowing the detection of more PFAS isomers and indicating promise toward future applications in chemical exposomics studies and biomarker discovery when molecules exhibit similar structures.

Bromine-Based Derivatization of Carboxyl-Containing Metabolites for Liquid Chromatography-Trapped Ion Mobility Spectrometry-Mass Spectrometry

The analysis of small carboxyl-containing metabolites (CCMs), such as tricarboxylic acid (TCA) cycle intermediates, provides highly useful information about the metabolic state of cells. However, their detection using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) methods can face sensitivity and specificity challenges given their low ionization efficiency and the presence of isomers. Ion mobility spectrometry (IMS), such as trapped ion mobility spectrometry (TIMS), provides additional specificity, but further signal loss can occur during the mobility separation process. We, therefore, developed a solution to boost CCM ionization and chromatographic separation as well as leverage specificity of IMS. Inspired by carbodiimide-mediated coupling of carboxylic acids with 4-bromo-N-methylbenzylamine (4-BNMA) for quantitative analysis, we newly report the benefits of this reagent for TIMS-based measurement. We observed a pronounced (orders of magnitude) increase in signal and enhanced isomer separations, particularly by LC. We found that utilization of a brominated reagent, such as 4-BNMA, offered unique benefits for untargeted CCM measurement. Derivatized CCMs displayed shifted mobility out of the metabolite and lipid region of the TIMS-MS space as well as characteristic isotope patterns, which were leveraged for data mining with Mass Spectrometry Query Language (MassQL) and indication of the number of carboxyl groups. The utility of our LC-ESI-TIMS-MS/MS method with 4-BMA derivatization was demonstrated via the characterization of alterations in CCM expression in bone marrow-derived macrophages upon activation with lipopolysaccharide. While metabolic reprogramming in activated macrophages has been characterized previously, especially with respect to TCA cycle intermediates, we report a novel finding that isomeric itaconic, mesaconic, and citraconic acid increase after 24 h, indicating possible roles in the inflammatory response.

Structural Characterization of Dimeric Perfluoroalkyl Carboxylic Acid Using Experimental and Theoretical Ion Mobility Spectrometry Analyses

Per- and polyfluoroalkyl substances (PFAS) are contaminants of increasing concern, with over seven million compounds currently inventoried in the PubChem PFAS Tree. Recently, ion mobility spectrometry has been combined with liquid chromatography and high-resolution mass spectrometry (LC-IMS-HRMS) to assess PFAS. Interestingly, using negative electrospray ionization, perfluoroalkyl carboxylic acids (PFCAs) form homodimers ([2M-H]-), a phenomenon observed with trapped, traveling wave, and drift-tube IMS. In addition to the limited research on their effect on analytical performance, there is little information on the conformations these dimers can adopt. This study aimed to propose most probable conformations for PFCA dimers. Based on qualitative analysis of how collision cross section (CCS) values change with the mass-to-charge ratio (m/z) of PFCA ions, the PFCA dimers were hypothesized to likely adopt a V-shaped structure. To support this assumption, in silico geometry optimizations were performed to generate a set of conformers for each possible dimer. A CCS value was then calculated for each conformer using the trajectory method with Lennard-Jones and ion-quadrupole potentials. Among these conformers, at least one of the ten lowest-energy conformers identified for each dimer exhibited theoretical CCS values within a ±2% error margin compared to the experimental data, qualifying them as plausible structures for the dimers. Our findings revealed that the fluorinated alkyl chains in the dimers are close to each other due to a combination of C-F···O=C and C-F···F-C stabilizing interactions. These findings, together with supplementary investigations involving environmentally relevant cations, may offer valuable insights into the interactions and environmental behavior of PFAS.

Rapid and Accurate Identification of Microorganisms Using Ion Mobility-Mass Spectrometry

Accurate identification of microorganisms to the strain and substrain levels in clinical and environmental samples is essential to provide an appropriate anti-biotherapy to the patients and reduce the prescription of broad-spectrum antimicrobials to minimize antibiotic resistance. Unfortunately, the current diagnosis methods are often slow, expensive, or laborious, which limits their use in resource-limited regions. Therefore, there is a strong unmet need for new technologies that can rapidly identify microorganisms in complex samples to complement the existing commercially available technologies. This Young Scientist Perspective demonstrates the value of combining the attributes of ion mobility-mass spectrometry and ambient ionization, enabling the rapid and accurate discrimination of bacteria to the species level after only a four-hour culturing period and showing that various bacterial species can have different isomers and conformers of their biomarkers. However, to discriminate closely-related bacterial strains, we needed to include other separation techniques in our workflow, such as liquid chromatography. Also, we utilized whole organism fingerprints, which include metabolites, lipids, and peptides, using our optimized workflow and machine learning to analyze a wide set of E. coli strains in artificially contaminated urine samples. Moreover, the various challenges for the routine identification of microorganisms using our optimized techniques in medical, environmental, and security fields and future outlooks are discussed.

Multidimensional Separations for Characterization of Isomeric PFAS Using SLIM High-Resolution Ion Mobility and Tandem Mass Spectrometry

Per- and polyfluoroalkyl substances (PFAS) are synthetic organofluorine compounds that accumulate in the environment due to significant industrial use and resistance to degradation. PFAS are of global interest because of their environmental and health concerns. They exist in a variety of linear and nonlinear forms containing a variety of isomers, as well as differing functional headgroups for each class. That structural complexity requires advanced analytical techniques, beyond current high-resolution mass spectrometry (HRMS) methods, for their accurate identification and quantification in a wide range of samples. Herein, we demonstrate the power of Structures for Lossless Ion Manipulations (SLIM)-based high-resolution ion mobility (HRIM) for separation of complex PFAS branched isomers. SLIM is integrated into a multidimensional LC-SLIM IM-MS/MS workflow, developed for the extensive characterization of a wide range of PFAS compounds. As we surveyed sulfonate and carboxylic acid classes of PFAS, we observed unique arrival time vs m/z trend lines that were representative of each class; these trend lines are important for allowing identification of emerging species based on their placement in that two-dimensional space. Next, we used complementary tandem mass spectrometry (MS/MS) approaches with all ion fragmentation (AIF), as well as energy-resolved MS/MS, to further investigate the structure of mobility-separated species. This allowed both investigation of fragmentation mechanism and identification of unique fragment ions that could allow differentiation of isomers when ion mobility was insufficient. Overall, the combination of chromatography, high-resolution SLIM, and MS/MS provided a comprehensive workflow capable of identifying unknown emerging PFAS compounds in complex environmental samples.

Exosomes Released from Senescent Cells and Circulatory Exosomes Isolated from Human Plasma Reveal Aging-associated Proteomic and Lipid Signatures

Senescence emerged as significant mechanism of aging and age-related diseases, offering an attractive target for clinical interventions. Senescent cells release a senescence-associated secretory phenotype (SASP), including exosomes that may act as signal transducers between distal tissues, propagating secondary or bystander senescence and signaling throughout the body. However, the composition of exosome SASP remains underexplored, presenting an opportunity for novel unbiased discovery. We present a detailed proteomic and lipidomic analysis of exosome SASP using mass spectrometry from human plasma from young and older individuals and from tissue culture of senescent primary human lung fibroblasts. We identified ∼1,300 exosome proteins released by senescent cells induced by three different senescence inducers. In parallel, a human plasma cohort from young (20-26 years) and old (65-74 years) individuals revealed over 1,350 exosome proteins and 171 plasma exosome proteins were regulated when comparing old vs young individuals. Of the age-regulated plasma exosome proteins, we observed 52 exosome SASP factors that were also regulated in exosomes from the senescent fibroblasts, including serine protease inhibitors (SERPINs), Prothrombin, Coagulation factor V, Plasminogen, and Reelin. 247 lipids were identified in exosome samples. Following senescence induction, identified phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins increased significantly indicating cellular membrane changes. Interestingly, significantly changed proteins were related to extracellular matrix remodeling and inflammation, both potentially detrimental pathways that can damage surrounding tissues and even induce secondary senescence. Our findings reveal mechanistic insights and potential senescence biomarkers, enabling a better approach to surveilling the senescence burden in the aging population and offering therapeutic targets for interventions.

Multidimensional-Constrained Suspect Screening of Hydrophobic Contaminants Using Gas Chromatography-Atmospheric Pressure Chemical Ionization-Ion Mobility-Mass Spectrometry

Suspect screening strives to rapidly monitor a large number of substances in a sample using mass spectral libraries. For hydrophobic organic contaminants (HOCs), these libraries are traditionally based on electron ionization mass spectra. However, with the growing use of state-of-the-art mass spectrometers, which often use alternative ionization approaches and separation techniques, new suspect screening workflows and libraries are urgently needed. This study established a new suspect screening library for 1,590 HOCs, including exact mass and a combination of measured and model-predicted values for retention time (RT) and collision cross section (CCS). The accuracy of in silico predictions was assessed using standards for 102 HOCs. Thereafter, using gas chromatography-atmospheric pressure chemical ionization-ion mobility-mass spectrometry, a suspect screening workflow constrained by the full scan mass spectrum of (quasi-)molecular ions (including isotope patterns), RT, CCS, and fragmentation mass spectra, together with a continuous scoring system, was established to reduce false positives and improve identification confidence. Application of the method to fortified and standard reference sediment samples demonstrated true positive rates of 79% and 64%, respectively, with all false positives attributed to suspect isomers. This study offers a new workflow for improved suspect screening of HOCs using multidimensional information and highlights the need to enrich mass spectral databases and extend the applicable chemical space of current in silico tools to hydrophobic substances.

Lipidomics reveals cell specific changes during pluripotent differentiation to neural and mesodermal lineages

Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipidomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins, and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.

In Silico Characterization of Glycan Ions from IM-MS Collision Cross Section

Ion mobility mass spectrometry (IM-MS) can assist in the identification of isobaric chemical analytes by exploiting the difference in their gas phase collision cross-section (CCS) property. In glycomics, reliable glycan characterization remains challenging, even with IM-MS, because of closely related isomeric species and the available binding arrangements of substituted monosaccharides, allowing for the formation of complex structures. Here, we present a computational procedure to obtain gas-phase structural information from the experimental IM-MS CCS data of carbohydrates. The workflow proceeds with high throughput charge modeling of glycan seed structures to determine the precise protonation or deprotonation site. The charge models were then screened by using density functional theory (DFT) to produce candidate charge states for conformation generation. An extensive conformational scoring of the glycan ions was performed quantum mechanically at the DFT D3-B3LYP/6-31G+(d,p) level for the negative mode, [M - H]-, and at the D3-B3LYP/6-31G(d,p) level for the positive mode, [M + H]+. For most of our test set, the computed CCS values from the final geometry optimized structures showed good agreement with experiment. We also demonstrated the capability of characterizing configurational and constitutional isomeric species. Altogether, we believe that the method we used in this work can be used to build a reliable theoretical reference database for glycans that can be used for experimental quality control and for assigning molecular structure to experimental IM-MS CCS information.

Reference Library for Suspect Non-targeted Screening of Environmental Toxicants Using Ion Mobility Spectrometry-Mass Spectrometry

As our health is affected by the xenobiotic chemicals we are exposed to, it is important to rapidly assess these molecules both in the environment and our bodies. Targeted analytical methods coupling either gas or liquid chromatography with mass spectrometry (GC-MS or LC-MS) are commonly utilized in current exposure assessments. While these methods are accepted as the gold standard for exposure analyses, they often require multiple sample preparation steps and more than 30 minutes per sample. This throughput limitation is a critical gap for exposure assessments and has resulted in an evolving interest in using ion mobility spectrometry and MS (IMS-MS) for non-targeted studies. IMS-MS is a unique technique due to its rapid analytical capabilities (millisecond scanning) and detection of a wide range of chemicals based on unique collision cross section (CCS) and mass-to-charge (m/z) values. To increase the availability of IMS-MS information for exposure studies, here we utilized drift tube IMS-MS to evaluate 4,685 xenobiotic chemical standards from the Environmental Protection Agency Toxicity Forecaster (ToxCast) program including pesticides, industrial chemicals, pharmaceuticals, consumer products, and per- and polyfluoroalkyl substances (PFAS). In the analyses, 3,993 [M+H]+, [M+Na]+, [M-H]- and [M+]+ ion types were observed with high confidence and reproducibility (≤1% error intra-laboratory and ≤2% inter-laboratory) from 2,140 unique chemicals. These values were then assembled into an openly available multidimensional database and uploaded to PubChem to enable rapid IMS-MS suspect screening for a wide range of environmental contaminants, faster response time in environmental exposure assessments, and assessments of xenobiotic-disease connections.

Structural characterisation and dynamics of a paramagnetic {Cr12Ni3} seahorse in non-crystalline phases

The complex [{Ni(cyclen)}2Cr12NiF18(O2CtBu)24] (where cyclen = 1,4,7,10-tetrazacyclododecane) crystallises as a fifteen-metal chain that is shaped like a seahorse. Given this is one of the longest finite, paramagnetic chains found, we were intrigued whether this unusual structure is induced during crystal growth or also maintained in other phases. We report electron paramagnetic resonance spectroscopy, small angle X-ray scattering and atomistic molecular dynamics simulations, demonstrating that the S-structure from crystal is stable in powder and solution. Using ion mobility mass spectrometry (IM-MS), we revealed the coexistence of S-shaped structures and a closed isomeric assembly in the gas phase. Collision-induced dissociation mass spectrometry studies monitored by IM-MS show the rearrangement of the cyclic seahorse to the S-shaped conformation, as well as the dissociation to a cyclic, seven-metal complex.

Development of an Oxylipin Library Using Liquid Chromatography-Ion Mobility Quadrupole Time-of-Flight: Application to Mouse Brain Tissue

Oxylipins are bioactive lipid mediators derived from polyunsaturated fatty acids (PUFAs) that play crucial roles in physiological and pathological processes. The analysis and identification of oxylipins are challenging due to the numerous isomeric forms. Ion mobility (IM), which separates ions based on their spatial configuration, combined with liquid chromatography (LC) and mass spectrometry (MS), has been proven effective for separating isomeric compounds. In this study, we developed an extensive oxylipin library containing information on retention time (RT), m/z, and CCS values for 74 oxylipin standards using LC-IM-QTOF-MS in positive and negative ionization modes. The oxylipins in the library were grouped into 15 isomer categories to evaluate the efficacy of IM in isomeric separation. Various adducts were investigated, including protonated, deprotonated, and sodiated forms. The ΔCCS% for more than 1000 isomeric pairs was calculated, revealing that 30% of these exhibited a ΔCCS% greater than 2%. Positive ionization mode demonstrated superior separation capabilities, with 274 isomer pairs achieving baseline separation (ΔCCS% >  4%). Sodium adducts significantly improved isomer separation. With the inclusion of LC separation, only nine oxylipins coeluted, forming six different isomeric pairs. CCS values for the adducts [M+Na]+ and [M+2Na-H]+ separated three of these isomeric pairs. The CCS values were compared to experimental libraries, confirming the high reproducibility of CCS measurements, with average errors below 2%. Applying this library to mouse brain samples, 19 different oxylipins were identified by matching RT, m/z, and CCS values. Coeluting isomers, 9- and 13-HODE, 8- and 12-HETE, and 15-oxo-ETE and 14(15)-EpETrE, were successfully separated and identified using drift time separation.

High-throughput screening of fentanyl analogs

This study presents an analytical approach coupling novel ambient ionization sources with trapped ion mobility spectrometry (TIMS) and tandem mass spectrometry (MS/MS) for the rapid characterization of fentanyl analogs. Two ambient ionization sources were illustrated for minimal sample preparation and rapid analysis: electrospray ionization (nESI) and direct analysis in real time (DART). Fentanyl analogs can be separated using nESI-TIMS-MS/MS based on differences in their mobility and/or fragmentation pattern; reference mobility spectra are reported for 234 single standards. In contrast, DART-TIMS-MS/MS allowed for the characterization of 201 compounds due to differences in the protonation pattern and efficiency when compared to nESI. The TIMS high resolving power (R > 80) allowed baseline separation for most isomers and mobility trends were established for methylated and fluorinated isomers, with the more compact ortho-substituted analogs showing distinct separation from para- and meta-substituted species. This multi-dimensional strategy offers a comprehensive characterization of fentanyl analogs and other synthetic opioids with minimal sample preparation. This analysis shows significant potential for high-throughput screening (<5 min) and high sensitivity detection ( Collapse

Key Words

• DART
• Fentanyl
• Identification
• Isomers
• Mobility
• Screening

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MESH Headings

• Fentanyl/analogs & derivatives
• Fentanyl/analysis
• Fentanyl/chemistry
• High-Throughput Screening Assays/methods
• Tandem Mass Spectrometry/methods
• Ion Mobility Spectrometry/methods
• Spectrometry, Mass, Electrospray Ionization/methods
• Analgesics, Opioid/analysis
• Analgesics, Opioid/chemistry

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Grants

• R01 GM134247 NIGMS NIH HHS
• R35 GM153450 NIGMS NIH HHS

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Affiliation(s)

Samuel A Miller Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, United States
Andrew R Forero Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, United States
Lilian Valadares Tose Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, United States
Jordan E Krechmer Bruker Daltonics Inc., Billerica, MA, 01821, United States
Felician Muntean Bruker Daltonics Inc., Billerica, MA, 01821, United States
Francisco Fernandez-Lima Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, United States.

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Updated Guidance for Communicating PFAS Identification Confidence with Ion Mobility Spectrometry

Over the last decade, global contamination from per- and polyfluoroalkyl substances (PFAS) has become apparent due to their detection in countless matrices worldwide, from consumer products to human blood to drinking water. As researchers implement non-targeted analyses (NTA) to more fully understand the PFAS present in the environment and human bodies, clear guidance is needed for consistent and objective reporting of the identified molecules. While confidence levels for small molecules analyzed and identified with high-resolution mass spectrometry (HRMS) have existed since 2014, unification and automation of these levels is needed due to inconsistencies in reporting and continuing innovations in analytical methods. Here, we (i) investigate current practices for confidence level reporting of PFAS identified with liquid chromatography (LC), gas chromatography (GC), and/or ion mobility spectrometry (IMS) coupled with high resolution mass spectrometry (HRMS) and (ii) propose a simple, unified confidence level guidance that incorporates both PFAS-specific attributes and IMS collision cross section (CCS) values.

Multidimensional library for the improved identification of per- and polyfluoroalkyl substances (PFAS)

As the occurrence of human diseases and conditions increase, questions continue to arise about their linkages to chemical exposure, especially for per-and polyfluoroalkyl substances (PFAS). Currently, many chemicals of concern have limited experimental information available for their use in analytical assessments. Here, we aim to increase this knowledge by providing the scientific community with multidimensional characteristics for 175 PFAS and their resulting 281 ion types. Using a platform coupling reversed-phase liquid chromatography (RPLC), electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI), drift tube ion mobility spectrometry (IMS), and mass spectrometry (MS), the retention times, collision cross section (CCS) values, and m/z ratios were determined for all analytes and assembled into an openly available multidimensional dataset. This information will provide the scientific community with essential characteristics to expand analytical assessments of PFAS and augment machine learning training sets for discovering new PFAS.

Face-controlled chirality induction in octahedral thiacalixarene-based porous coordination cages

Nanosized chiral octahedral M32 coordination cages were prepared via self-assembly of sulfonylcalix[4]arene tetranuclear M(II) clusters (M = Co or Ni) with enantiomerically enriched linkers based on tris(dipyrrinato)cobalt(III) complexes, appended with peripheral carboxylic groups. Two pairs of enantiomers of cages were obtained and unambiguously characterized from a structural point of view, using single crystal X-ray diffraction. Chiral-HPLC was used to evidence the enantiomers. In the solid state, the compounds present intrinsic and extrinsic porosity: the intrinsic porosity is linked with the size of the cages, which present an inner diameter of ca. 19 Å. The obtained solid-state supramolecular architectures demonstrated good performances as adsorbents for water and 2-butanol guest molecules.

Introducing "Identification Probability" for Automated and Transferable Assessment of Metabolite Identification Confidence in Metabolomics and Related Studies

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence─the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in the context of the chemical space being considered. Neither are they easily automated nor transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/N, where N is the number of compounds in a database that matches an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multiproperty reference libraries constructed from a subset of the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.

Lanthanide chloride clusters, LnxCl3x+1-, x = 1-6: an ion mobility and DFT study of isomeric structures and interconversion timescales

Ion mobility spectrometry (IMS) (also including IMS-IMS measurements) as well as DFT calculations have been used to study isomer distributions and isomer interconversion in a range of electrospray-generated lanthanide chloride cluster anions, LnxCl3x+1- (where x = 1-6, and Ln corresponds to the 15 lanthanide elements (except for radioactive Pm)). Where measurement and structural rearrangement timescales allow, we obtain almost quantitative agreement between experiment and theory thus confirming isomer predictions and reproducing isomer intensity ratios. LnxCl3x+1- structures reflect strong ionic bonding with limited directionality. Ring and chain motifs dominate for smaller clusters while for larger clusters more compact three-dimensional structures become favourable. At cluster sizes with two or more closely lying isomers, the lanthanide contraction can lead to systematic variations in structure types across the series.

Roughhousing with Ions: Surface-Induced Dissociation and Electron Capture Dissociation as Diagnostics of Q-Cyclic IMS-TOF Instrument Tuning Gentleness

Native mass spectrometry can characterize a range of biomolecular features pertinent to structural biology, including intact mass, stoichiometry, ligand-bound states, and topology. However, when an instrument's ionization source is tuned to maximize signal intensity or adduct removal, it is possible that the biomolecular complex's tertiary and quaternary structures can be rearranged in a way that no longer reflect its native-like conformation. This could affect downstream ion activation experiments, leading to erroneous conclusions about the native-like structure. One activation strategy is surface-induced dissociation (SID), which generally causes native-like protein complexes to dissociate along the weakest subunit interfaces, revealing critical information about the complex's native-like topology and subunit connectivity. If the quaternary structure has been disturbed, then the SID fingerprint will shift as well. Thus, SID was used to diagnose source-induced quaternary structure rearrangement and help tune an instrument's source and other upstream transmission regions to strike the balance between signal intensity, adduct removal, and conserving the native-like structure. Complementary to SID, electron-capture dissociation (ECD) can also diagnose rearranged quaternary structures and was used after in-source activation to confirm that the subunit interfaces were rearranged, opening the structure to electron capture and subsequent dissociation. These results provide a valuable guide for new practitioners of native mass spectrometry and highlight the importance of using standard protein complexes when tuning new instrument platforms for optimal native mass spectrometry performance.

Identification and Structural Elucidation of Acylsugars in Tomato Leaves Using Liquid Chromatography-Ion Mobility-Tandem Mass Spectrometry (LC-IM-MS/MS)

Leaves of tomato plants contain various glandular trichomes that produce a wide range of metabolic products including acylsugars, which may serve as a defense mechanism against various insect pests. Acylsugars exhibit significant structural diversity, differing in their sugar cores, acylated positions, and type of acyl chains. This work demonstrated a comprehensive approach using multidimensional separation techniques, specifically liquid chromatography-ion mobility-tandem mass spectrometry (LC-IM-MS/MS), for structural characterization, and the discrimination of different tomato plants (one cultivar and five accessions) was demonstrated using tomato leaf extracts; six genotypes from five species of Solanum were represented. As a result, we identified 16 acylsugars through their molecular formulas and annotations using LC and MS analyses. The incorporation of ion mobility (IM) analysis revealed an additional 9 isomeric forms, resulting in a comprehensive total of 25 isomeric acylsugars identified. Furthermore, the experimental collision cross section (CCSexp) values agreed reasonably well with the corresponding predicted values (CCSpred), with an overall estimated error of less than 2%. These findings pave the way for research into how the different structural isomers of acylsugars might influence the self-defense mechanism in plants. Moreover, this work demonstrated that the investigated cultivar and accessions of tomatoes can be distinguished from each other based on their metabolite profile, e.g., acylsugars, with principal component analysis (PCA) and linear discriminant analysis (LDA) statistical models, yielding a prediction rate of 98.3%.

Lipidomics Reveals Cell Specific Changes During Pluripotent Differentiation to Neural and Mesodermal Lineages

Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipdiomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.

Rounded Turn SLIM Design for High-Resolution Ion Mobility Mass Spectrometry Analysis of Small Molecules

Various rounded turn designs in Structures for Lossless Ion Manipulation (SLIM) were explored via ion trajectory simulations. The optimized design was integrated into a SLIM ion mobility (IM) system coupled with a time-of-flight (TOF) mass spectrometer (MS) for further experimental investigation. The SLIM-TOF IM-MS system was assessed for IM resolution and ion transmission efficiency across a wide m/z range using various RF frequencies and buffer gas combinations. High ion transmission efficiency and high resolution ion mobility (HRIM) separation were achieved for Agilent tune mix ions through a ∼12.8 m serpentine separation path in both nitrogen and helium. In helium, ion transmission for low m/z ions was enhanced at higher RF trapping frequency, enabling the detection of ions with m/z below 50 and all 17 amino acids from a standard mixture. Lossless ion transmission was observed for glycine (m/z 76) in both passthrough and HRIM modes. HRIM resolution was benchmarked using L-isoleucine, L-leucine, and various other isobaric and isomeric metabolites with m/z values of 60-89. This work demonstrates a rounded turn SLIM design that enables HRIM measurements for small molecule analytes, with a particular focus on metabolomics, where IM offers a means to enhance the speed, robustness, and specificity of analytical workflows.

Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions

Domoic acid is a neurotoxin secreted by the marine diatom genus Pseudo-nitzschia during toxic algal bloom events. California sea lions (Zalophus californianus) are exposed to domoic acid through the ingestion of fish that feed on toxic diatoms, resulting in domoic acid toxicosis (DAT), which can vary from mild to fatal. Sea lions with mild disease can be treated if toxicosis is detected early after exposure. Therefore, rapid diagnosis of DAT is essential but also challenging. In this work, we performed multiomics analyses, specifically proteomic and lipidomic, on blood samples from 31 California sea lions. Fourteen sea lions were diagnosed with DAT based on clinical signs and post-mortem histological examination of brain tissue, and 17 had no evidence of DAT. Proteomic analyses revealed 31 statistically significant proteins in the DAT individuals compared to the non-DAT individuals (adjusted p < 0.05). Of these proteins, 19 were decreased in the DAT group of which three were apolipoproteins that are known to transport lipids in the blood, prompting lipidomic analyses. In the lipidomic analyses, 331 lipid species were detected with high confidence and multidimensional separations, and 29 were found to be statistically significant (adjusted p < 0.05 and log2(FC) < -1 or >1) in the DAT versus non-DAT comparison. Of these, 28 were lower in the DAT individuals, while only 1 was higher. Furthermore, 15 of the 28 lower concentration lipids were triglycerides, illustrating their putative connection with the perturbed apolipoproteins and potential use in rapid DAT diagnoses.

Characterization of Anticancer Drug Protomers Using Electrospray Ionization and Ion Mobility Spectrometry-Mass Spectrometry

We used electrospray ionization and ion mobility spectrometry-mass spectrometry to detect and characterize the three anticancer drugs palbociclib, copanlisib, and olaparib. Ion mobility-mass spectrometry and density functional theory revealed that these compounds generate isomers during ionization (protomers) due to the presence of multiple protonation sites within their chemical structures. Our work has implications for understanding the solution- and gas-phase chemistry of these molecules during spray-based ionization processes.

Molecular insights into the interaction between a disordered protein and a folded RNA

Intrinsically disordered protein regions (IDRs) are well established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, Small ERDK-Rich Factor (SERF). At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein- and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 Trans-Activation Response (TAR) RNA with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation.

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.

Ion Mobility-Mass Spectrometry Captures the Structural Consequences of Lipid Nanoparticle Encapsulation on Ribonucleic Acid Cargo

Ribonucleic acids (RNAs) are becoming increasingly significant in our search for improved biotherapeutics. RNA-based treatments offer high specificity, targeted delivery, and potentially lower-cost options for various debilitating human diseases. Despite these benefits, there are still relatively few FDA-approved RNA-based therapies, with the notable exceptions being the mRNA (mRNA) COVID-19 vaccines, which are delivered using lipid nanoparticle (LNP) systems. LNPs are distinctive drug delivery systems (DDSs) because of their ability to target specific cells, their biocompatibility, and their efficiency in merging with cellular membranes to enhance treatment effectiveness. While the biophysical landscapes of RNA structures in solution are relatively well understood, the impact of the LNP environment on RNA remains less clear. This study uses native ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) techniques to investigate how LNP encapsulation affects RNA structure and stability. We examine how various factors, such as ionization polarity, cofactor binding, lipid types, and lipid ratios, influence LNP-released RNA cargo. Our findings reveal that LNP DDSs induce significant changes in the structures and stabilities of their RNA cargo. However, the extent of these changes strongly depends on the type and composition of the lipids used. We conclude by discussing how IM-MS and CIU can aid in the continued development of more efficient LNP DDSs and improve DDS selection methodologies overall.

Influence of symmetry breaking on the absorption spectrum of crystal violet: from isolated cations at 5 K to room temperature solutions

We report the resolution of a long-standing puzzle in molecular spectroscopy: the origin of the shoulder in the room temperature solution absorption spectrum of crystal violet (CV) - an archetypal cationic triphenylmethane dye. This was achieved by comparing experimental and theoretical results for CV in solution at room temperature and as an isolated cation in gas-phase at 5 K. The two lowest energy electronically excited states involved in the visible region absorption are degenerate and coupled via a Jahn-Teller (JT) mechanism involving phenyl torsions, making CV particularly sensitive to environmental perturbations. The shoulder is absent in the low-temperature isolated cation spectrum, and vibronic simulations based on time dependent density functional theory (TD-DFT) indicate negligible JT effects under these conditions. Combining vibronic simulations with molecular dynamics, demonstrates that in water and toluene solution at room temperature the shoulder arises mainly from an intermolecular, Jahn-Teller-like symmetry-breaking effect induced by the fluctuating electrostatic potential of the disordered solvent environment, rather than from molecular distortions.

Trapped and drift-tube ion-mobility spectrometry for the analysis of environmental contaminants: Comparability of collision cross-section values and resolving power

RATIONALE

Ion-mobility (IM)-derived collision cross-section (CCS) values can serve as a valuable additional identification parameter within suspect and non-target screening studies of environmental contaminants. However, these applications require to assess the reproducibility of CCS calculations between different IM set-ups. Especially for the comparison of trapped and drift-tube IM (TIMS/DTIM) derived CCS values, data for environmental applications is lacking.

METHODS

The presented study assessed the bias of TIMS derived CCSN2 (TIMSCCSN2) values of 48 environmental contaminants from three classes in comparison to a previously established DTIM database. Based on two sets of isomeric bisphenols, the resolving power of both systems was compared, addressing the instrumental settings which influence the resolution of TIMS measurements.

RESULTS

For 91% of the datapoints, bias between TIMSCCSN2 and DTCCSN2 values (latter set as reference) were < 2%, indicating a good inter-platform reproducibility. TIMS resolving power was dependent on the selected mobility window and ramping times whereby a resolution of up to 116 was achieved. Similar resolving power was observed for multiplexed DTIMS data if a high-resolution post-processing step was implemented.

CONCLUSIONS

These results provide valuable insights in CCSN2 reproducibility facilitating database transfer in future TIMS based studies. Knowledge on the influence of acquisition settings on robustness of TIMSCCSN2 calculations and resolving power can ease method development supporting efficient development and reliable identifications of emerging environmental contaminants.

Leveraging High-Resolution Ion Mobility-Mass Spectrometry for Cyclic Peptide Soft Spot Identification

Cyclic peptides are an important class of molecules that gained significant attention in the field of drug discovery due to their unique pharmacological characteristics and enhanced proteolytic stability. Yet, gastrointestinal degradation remains a major hurdle in the discovery of orally bioavailable cyclic peptides. Soft spot identification (SSID) of the regions in the cyclic peptide sequence susceptible to amide hydrolysis by proteases is used in the discovery stage to guide medicinal chemistry design. SSID can be an arduous task, traditionally performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS), often resulting in complex and time-consuming manual analysis, particularly when isomeric linear peptide metabolites chromatographically coelute. Here, we present an alternative orthogonal approach that entails a high-resolution ion mobility (HRIM) system based on Structures for Lossless Ion Manipulation (SLIM) technology interfaced with quadrupole time-of-flight (QTOF) mass spectrometry to address some of the challenges associated with SSID. Two strategies were used to resolve linear isomeric peptide metabolites: labeled and label-free, both utilizing the HRIM platform. The label-free strategy leverages negative polarity to ionize the isomers which achieves better separation of the gas phase ions in the ion mobility (IM) dimension as compared to positive polarity, which is a more conventional approach when studying proteins and peptides. The second approach uses an isotope-labeled dimethyl tag on the terminal amine group, acting as a "shift reagent" to influence the mobility of isomers in the positive mode. This method resulted in baseline separation for the isomers of interest and produced unique product ions in the fragmentation spectra for unambiguous soft spot identification. Both label-free and labeled strategies demonstrated the ability to solve the challenges associated with SSID for cyclic peptides.

Discrimination of Common E. coli Strains in Urine by Liquid Chromatography-Ion Mobility-Tandem Mass Spectrometry and Machine Learning

Accurate identification of bacterial strains in clinical samples is essential to provide an appropriate antibiotherapy to the patient and reduce the prescription of broad-spectrum antimicrobials, leading to antibiotic resistance. In this study, we utilized the combination of a multidimensional analytical technique, liquid chromatography-ion mobility-tandem mass spectrometry (LC-IM-MS/MS), and machine learning to accurately identify and distinguish 11 Escherichia coli (E. coli) strains in artificially contaminated urine samples. Machine learning was utilized on the LC-IM-MS/MS data of the inoculated urine samples to reveal lipid, metabolite, and peptide isomeric biomarkers for the identification of the bacteria strains. Tandem MS and LC separation proved effective in discriminating diagnostic isomers in the negative ion mode, while IM separation was more effective in resolving conformational biomarkers in the positive ion mode. Using hierarchical clustering, the strains are clustered accurately according to their group highlighting the uniqueness of the discriminating biomarkers to the class of each E. coli strain. These results show the great potential of using LC-IM-MS/MS and machine learning for targeted omics applications to diagnose infectious diseases in various environmental and clinical samples accurately.

High Resolution Ion Mobility Enables the Structural Characterization of Atropisomers of GDC-6036, a KRAS G12C Covalent Inhibitor

GDC-6036 is a covalent KRAS G12C inhibitor that demonstrates high potency and selectivity. Structurally, GDC-6036 consists of several motifs that make the analytical characterization of this molecule challenging, including a highly basic pyrrolidine motif bonded to a quinazoline ring via an ether bond and an atropisomeric carbon-carbon bond between functionalized pyridine and quinazoline groups. Structurally, the desired atropisomer was synthesized via an atroposelective Negishi coupling with very high yield. However, having a direct way to analyze and confirm the presence of the atropisomeric species remained challenging in routine analytical workflows. In this study, both variable temperature nuclear magnetic resonance (VT-NMR) and two different approaches of in-line ion mobility coupled to liquid chromatography mass spectrometry (LC-MS) workflows were evaluated for the characterization of GDC-6036 and its undesired atropisomer (Compound B) to support synthetic route development. Briefly, both VT-NMR and traveling wave ion mobility spectrometry (TWIMS) enabled by structures for lossless ion manipulation (SLIM) technology coupled to high resolution MS (HRMS) are able to elucidate the structures of the atropisomers in a complex mixture. Drift tube IMS (DTIMS) was also evaluated, but lacked the resolving power to demonstrate separation between the two species in a mixture, but did show slight differences in their arrival times when multiplexed and injected separately. The determined resolving power (Rp) by multiplexing the ions via DTIMS was 67.3 and 60.5 for GDC-6036 and Compound B, respectively, while the two peak resolving power (Rpp) was determined to be 0.41, indicating inadequate resolution between the two species. Alternatively, the SLIM-IM studies showed Rp of 103.8 and 99.4, with a Rpp of 2.64, indicating good separation between the atropisomers. Furthermore, the CCS/z for GDC-6036 and Compound B was determined to be 231.2 Å2/z and 235.0 Å2/z, respectively. Quantitative experiments demonstrate linearity (R2 >0.99) for both GDC-6036 and Compound B while maintaining separation via SLIM-IM. Spike recoveries of one atropisomer relative to the other yielded strong recoveries (98.7% to 102.5%) while maintaining reproducibility (<7% RSD). The study herein describes the analytical process for evaluating new technologies and strategies for implementation in routine biopharmaceutical characterization workflows.

Collision cross sections of large positive fullerene molecular ions and their use as ion mobility calibrants in trapped ion mobility mass spectrometry

Positive-ion laser desorption/ionization (LDI) of fullerenes contained in soot as produced by the Krätschmer-Huffman process delivers a wide range of fullerene molecular ions from C56+• to above C300+•. Here, the collision cross section (CCS) values of those fullerene molecular ions are determined using a trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) instrument. While CCS values in the range from C60+• to C96+• are already known with high accuracy, those of ions from C98+• onward had yet to be determined. The fullerene molecular ions covered in this work have CCS values from about 200 to 440 Å2. The fullerene molecular ion series is evenly spaced at C2 differences in composition, and thus, small CCS differences of just 2.2-3.5 Å2 were determined across the entire range. Fullerene M+• ions may be employed as mobility calibrants, in particular, when very narrow 1/K0 ranges are being analyzed to achieve high TIMS resolving power. In addition, due to the simple elemental composition, M+• ions of fullerenes could also serve for mass calibration. This study describes the determination of CCS values of fullerene molecular ions from C56+• to C240+• and the application of ions from C56+• to C220+• to calibrate the ion mobility scale of a Bruker timsTOFflex instrument in any combination of LDI, matrix-assisted laser desorption/ionization (MALDI), and electrospray ionization (ESI) modes in the CCS range from about 200 to 420 Å2. This use was exemplified along with ions from Agilent Tune Mix, leucine-enkephalin, angiotensin I, angiotensin II, and substance P.

Rapid separation of bile acid isomers via ion mobility mass spectrometry by complexing with spiramycin

Bile acid (BA) is one of the main active components of bile and has multiple isomers, the structure or content of its isomers often changes due to diseases and other health problems; thus, the accurate detection of BA isomers is very important. In this study, two groups of BA isomers of glycine-conjugated BAs and taurine-conjugated BAs were simultaneously separated and quantitatively analyzed by ion mobility mass spectrometry (IM-MS). Especially, baseline mobility separation between the isomers was achieved by the formation of binary complexes via simple interaction with spiramycin (SPM), for which a separation resolution (Rp-p) of 1.96 was reached. Moreover, BA isomers were quantitatively analyzed, and the limit of detection (LOD) of absolute quantification for TCDCA/TUDCA and GUDCA/GCDCA/GHDCA was 0.514 and 0.611 ng∙mL-1, respectively; the LODs for molar ratio ranges of relative quantification for TCDCA/TUDCA, GUDCA/GHDCA, and GCDCA/GHDCA were 1:18-30:1, 1:18-21:1, and 1:19-21:1, respectively. Additionally, BA isomers analyzed in pig bile powder and bear bile powder were measured, which were in good consistency with those labeled, revealing the differences in BA composition and content between the two powders. Finally, BA detection and recovery analyses were performed on serum samples, with a recovery rate of ≥73.69%, RSD of ≤6.8%, and SR (standard deviation of recoveries, the degree of difference between measured values and average recovery) of ≤1.27. Due to the simple, rapid, and lack of need for complex sample preparation and chromatographic separation, the proposed method can be an effective method for BA detection in practical samples.

Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection

Recurrent C. difficile infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we use longitudinal stool samples collected from patients undergoing FMT to evaluate intra-individual changes in the microbiome, metabolome, and lipidome after successful FMTs relative to their baselines pre-FMT. We show changes in the abundance of many lipids, specifically a decrease in acylcarnitines post-FMT, and a shift from conjugated bile acids pre-FMT to deconjugated secondary bile acids post-FMT. These changes correlate with a decrease in Enterobacteriaceae, which encode carnitine metabolism genes, and an increase in Lachnospiraceae, which encode bile acid altering genes such as bile salt hydrolases (BSHs) and the bile acid-inducible (bai) operon, post-FMT. We also show changes in gut microbe-encoded amino acid biosynthesis genes, of which Enterobacteriaceae was the primary contributor to amino acids C. difficile is auxotrophic for. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT and generate hypotheses that require further experimental validation. This information is meant to help guide the development of new microbiota-focused therapeutics to treat rCDI.IMPORTANCERecurrent C. difficile infection is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant. However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae pre-FMT, which encodes carnitine metabolism genes, and Lachnospiraceae post-FMT, which encodes bile salt hydrolases and baiA genes. There was also a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT, which we hope will help aid in the development of new microbiota-focused therapeutics to treat rCDI.

Eliminating the Deadwood: A Machine Learning Model for CCS Knowledge-Based Conformational Focusing for Lipids

Accurate elucidation of gas-phase chemical structures using collision cross section (CCS) values obtained from ion-mobility mass spectrometry benefits from a synergism between experimental and in silico results. We have shown in recent work that for a molecule of modest size with a proscribed conformational space we can successfully capture a conformation(s) that can match experimental CCS values. However, for flexible systems such as fatty acids that have many rotatable bonds and multiple intramolecular London dispersion interactions, it becomes necessary to sample a much greater conformational space. Sampling more conformers, however, accrues significant computational cost downstream in optimization steps involving quantum mechanics. To reduce this computational expense for lipids, we have developed a novel machine learning (ML) model to facilitate conformer filtering according to the estimated gas-phase CCS values. Herein we report that the implementation of our CCS knowledge-based approach for conformational sampling resulted in improved structure prediction agreement with experiment by achieving favorable average CCS prediction errors of ∼2% for lipid systems in both the validation set and the test set. Moreover, most of the gas-phase candidate conformations obtained by using CCS focusing achieved lower energy-minimum geometries than the candidate conformations without focusing. Altogether, the implementation of this ML model into our modeling workflow has proven to be beneficial for both the quality of the results and the turnaround time. Finally, while our approach is limited to lipids, it can be readily extended to other molecules of interest.

Evaluating Solid Phase Adsorption Toxin Tracking (SPATT) for passive monitoring of per- and polyfluoroalkyl substances (PFAS) with Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS)

Detection and monitoring of per- and polyfluoroalkyl substances (PFAS) in aquatic environments has become an increasingly higher priority of regulatory agencies as public concern for human intake of these chemicals continues to grow. While many methods utilize active sampling strategies ("grab samples") for precise PFAS quantitation, here we evaluate the efficacy of low-cost passive sampling devices (Solid Phase Adsorption Toxin Tracking, or SPATTs) for spatial and temporal PFAS assessment of aquatic systems. For this study, passive samplers were initially deployed in North Carolina along the Cape Fear River during the summer and fall of 2016 and 2017. These were originally intended for the detection of microcystins and monitoring potentially harmful algal blooms, though this period also coincided with occurrences of PFAS discharge from a local fluorochemical manufacturer into the river. Additional samplers were then deployed in 2022 to evaluate changes in PFAS fingerprint and abundances. Assessment of PFAS showed legacy compounds were observed across almost all sampling sites over all 3 years (PFHxS, PFOS, PFHxA, etc.), while emerging replacement PFAS (e.g., Nafion byproducts) were predominantly localized downstream from the manufacturer. Furthermore, samplers deployed downstream from the manufacturer in 2022 noted sharp decreases in observed signal for replacement PFAS in comparison to samplers deployed in 2016 and 2017, indicating mitigation and remediation efforts in the area were able to reduce localized fluorochemical contamination.

Targeted metabolomics assisted rapid screening and characterization of aristolochic acids and their DNA adducts in aristolochia plants by ultra-high performance liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry

Aristolochic acids are one of the major compounds in aristolochia plants, which are nephrotoxic and carcinogenic. A method was established for the detection and identification of aristolochic acids and their DNA adducts in four different herbs using ultra-high performance liquid chromatography-ion mobility quadrupole time-of flight mass spectrometry. Solid phase extraction conditions were optimized to improve the sensitivity of the experiment by using 40 mg of C18 as adsorbent and 100 μL ethanol as elution solvent. At a collision energy of 10-40 eV, these compounds and cleavage patterns were precisely identified and analyzed by secondary fragmentation and collision cross section values. The obtained mass spectrometry data were then analyzed by targeted metabolomics, including principal component analysis, partial least squares-discriminant analysis and hierarchical clustering analysis, and importing the samples in the established model, the confidence values can reach 0.61 and 0.76. All in all, this method can provide a useful tool for the detection of aristolochic acids and deoxyribonucleic acid adducts. In conclusion, this method was successfully used for the detection and identification of aristolochic acids and their DNA adducts.

Streamlining Phenotype Classification and Highlighting Feature Candidates: A Screening Method for Non-Targeted Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) Data

Nontargeted analysis (NTA) is increasingly utilized for its ability to identify key molecular features beyond known targets in complex samples. NTA is particularly advantageous in exploratory studies aimed at identifying phenotype-associated features or molecules able to classify various sample types. However, implementing NTA involves extensive data analyses and labor-intensive annotations. To address these limitations, we developed a rapid data screening capability compatible with NTA data collected on a liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) platform that allows for sample classification while highlighting potential features of interest. Specifically, this method aggregates the thousands of IMS-MS spectra collected across the LC space for each sample and collapses the LC dimension, resulting in a single summed IMS-MS spectrum for screening. The summed IMS-MS spectra are then analyzed with a bootstrapped Lasso technique to identify key regions or coordinates for phenotype classification via support vector machines. Molecular annotations are then performed by examining the features present in the selected coordinates, highlighting potential molecular candidates. To demonstrate this summed IMS-MS screening approach, we applied it to clinical plasma lipidomic NTA data and exposomic NTA data from water sites with varying contaminant levels. Distinguishing coordinates were observed in both studies, enabling the evaluation of phenotypic molecular annotations and resulting in screening models capable of classifying samples with up to a 25% increase in accuracy compared to models using annotated data.

Identifying and Quantifying Relative Concentrations of Epimers in Mixtures via Cyclic Ion Mobility Mass Spectrometry: Dexamethasone and Betamethasone as a Case Study

Epimers can show different biological activities and different pharmacological behaviors; therefore, their separation and analysis are crucial in the drug development process. Due to their similar chemical and physical properties, separation of epimers is challenging. This study demonstrates the application of cyclic ion mobility-mass spectrometry to separate, identify, and quantify dexamethasone and betamethasone in a binary mixture. Cyclic IMS separation of the isolated protonated dimer resulted in three peaks: dexamethasone homodimer, betamethasone homodimer, and their heterodimer. Besides providing improved separation over the protonated monomer, the presence of a heterodimer peak provides additional confirmation of an isomeric mixture. We identified the dexamethasone and betamethasone homodimer peaks by infusing pure solutions of each epimer and measuring each pure homodimer's arrival time. The measured peak areas indicated that the heterodimer is formed at twice the rate of each homodimer and that dexamethasone and betamethasone contribute equally to the heterodimer signal. Using this observation, we could accurately calculate the relative concentrations of each epimer by adding half of the heterodimer peak area to each homodimer peak area. These findings enable the identification and quantification of dexamethasone and betamethasone based on the arrival time distributions of their protonated dimers. This is the first demonstration of accurate relative quantification of epimers by separating charged dimers in the gas phase.

An Untargeted Lipidomics Workflow Incorporating High-Resolution Demultiplexing (HRdm) Drift Tube Ion Mobility-Mass Spectrometry

Global discovery lipidomics can provide comprehensive chemical information toward understanding the intricacies of metabolic lipid disorders such as dyslipidemia; however, the isomeric complexity of lipid species remains an analytical challenge. Orthogonal separation strategies, such as ion mobility (IM), can be inserted into liquid chromatography-mass spectrometry (LC-MS) untargeted lipidomic workflows for additional isomer separation and high-confidence annotation, and the emergence of high-resolution ion mobility (HRIM) strategies provides marked improvements to the resolving power (Rp > 200) that can differentiate small structural differences characteristic of isomers. One such HRIM strategy, high-resolution demultiplexing (HRdm), utilizes multiplexed drift tube ion mobility spectrometry (DTIMS) with post-acquisition algorithmic deconvolution to access high IM resolutions while retaining the measurement precision inherent to the drift tube technique; however, HRdm has yet to be utilized in untargeted studies. In this manuscript, a proof-of-concept study using ATP10D dysfunctional murine models was investigated to demonstrate the utility of HRdm-incorporated untargeted lipidomic analysis pipelines. Total lipid features were found to increase by 2.5-fold with HRdm compared to demultiplexed DTIMS as a consequence of more isomeric lipids being resolved. An example lipid, PC 36:5, was found to be significantly higher in dysfunctional ATP10D mice with two resolved peaks observed by HRdm that were absent in both the functional ATP10D mice and the standard demultiplexed DTIMS acquisition mode. The benefits of utilizing HRdm for discerning isomeric lipids in untargeted workflows have the potential to enhance our analytical understanding of lipids related to disease complexity and biologically relevant studies.

Revisiting Dissolved Organic Matter Analysis Using High-Resolution Trapped Ion Mobility and FT-ICR Mass Spectrometry

The molecular level characterization of complex mixtures remains an analytical challenge. We have shown that the integration of complementary, high-resolution, gas-phase separations allows for chemical formula level isomeric content description. In the current work, we revisited the current challenges associated with the analysis of dissolved organic matter using high-resolution trapped ion mobility separation (TIMS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). In particular, we evaluated the separation capabilities provided by TIMS-MS compared to MS alone, the use of ICR complementary data acquisition (DAQ) systems and transient processing strategies, ICR cell geometries (e.g., Infinity cell vs harmonized cell), and magnetic field strengths (7 T vs 9.4 T vs 21 T) for the case of a Harney River DOM sample. Results showed that the external high-performance DAQ enables direct representation of mass spectra in absorption mode FT (aFT), doubling the MS resolution compared to the default magnitude mode FT (mFT). Changes between half- vs full-apodization result in greater MS signal/noise vs superior MS resolving power (RP); in the case of DOM analysis, a 45% increase in assigned formulas is observed when employing the DAQ half (Kaiser-type)-apodization window and aFT when compared to the default instrument mFT. Results showed the advantages of reprocessing 2D-TIMS-FT-ICR MS data with higher RP and magnetic field chemical formulas generated list acquired (e.g., 21 T led to a 24% increase in isomers reported) or the implementation of alternative strategies.

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.

Recent additions and access to a multidimensional lipidomic database containing liquid chromatography, ion mobility spectrometry, and tandem mass spectrometry information

The importance of lipids in biology continues to grow with their recent linkages to more diseases and conditions, microbiome fluctuations, and environmental exposures. These associations have motivated researchers to evaluate lipidomic changes in numerous matrices and studies. Lipidomic analyses, however, present numerous challenges as lipid species have broad chemistries that require different extraction methods and instrumental analyses to evaluate and separate their many isomers and isobars. Increasing knowledge about different lipid characteristics is therefore crucial for improving their separation and identification. Here, we present a multidimensional database for lipids analyzed on a platform combining reversed-phase liquid chromatography, drift tube ion mobility spectrometry, collision-induced dissociation, and mass spectrometry (RPLC-DTIMS-CID-MS). This platform and the different separation characteristics it provides enables more confident lipid annotations when compared to traditional tandem mass spectrometry platforms, especially when analyzing highly isomeric molecules such as lipids. This database expands on our previous publication containing only human plasma and bronchoalveolar lavage fluid lipids and provides experimental RPLC retention times, IMS collision cross section (CCS) values, and m/z information for 877 unique lipids from additional biofluids and tissues. Specifically, the database contains 1504 precursor [M + H]+, [M + NH4]+, [M + Na]+, [M-H]-, [M-2H]2-, [M + HCOO]-, and [M + CH3COO]- ion species and their associated CID fragments which are commonly targeted in clinical and environmental studies, in addition to being present in the chloroform layer of Folch extractions. Furthermore, this multidimensional RPLC-DTIMS-CID-MS database spans 5 lipid categories (fatty acids, sterols, sphingolipids, glycerolipids, and glycerophospholipids) and 24 lipid classes. We have also created a webpage (tarheels.live/bakerlab/databases/) to enhance the accessibility of this resource which will be populated regularly with new lipids as we identify additional species and integrate novel standards.

Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions

Domoic acid is a neurotoxin secreted by the marine diatom genus, Pseudo-nitzschia , during toxic algal bloom events. California sea lions ( Zalophus californianus ) are exposed to domoic acid through ingestion of fish that feed on toxic diatoms, resulting in a domoic acid toxicosis (DAT), which can vary from mild to fatal. Sea lions with mild disease can be treated if toxicosis is detected early after exposure, therefore, rapid diagnosis of DAT is essential but also challenging. In this work, we performed multi-omics analyses, specifically proteomic and lipidomic, on blood samples from 31 California sea lions. Fourteen sea lions were diagnosed with DAT based on clinical signs and postmortem histological examination of brain tissue, and 17 had no evidence of DAT. Proteomic analyses revealed three apolipoproteins with statistically significant lower abundance in the DAT individuals compared to the non-DAT individuals. These proteins are known to transport lipids in the blood. Lipidomic analyses highlighted 29 lipid levels that were statistically different in the DAT versus non-DAT comparison, 28 of which were downregulated while only one was upregulated. Furthermore, of the 28 downregulated lipids, 15 were triglycerides, illustrating their connection with the perturbed apolipoproteins and showing their potential for use in rapid DAT diagnoses.

SYNOPSIS

Multi-omics evaluations reveal blood apolipoproteins and triglycerides are altered in domoic acid toxicosis in California sea lions.

GRAPHIC ABSTRACT