Native ion mobility-mass spectrometry reveals the binding mechanisms of anti-amyloid therapeutic antibodies.

One of the most important attributes of anti-amyloid antibodies is their selective binding to oligomeric and amyloid aggregates. However, current methods of examining the binding specificities of anti-amyloid ß (Aß) antibodies have limited ability to differentiate between complexes that form between antibodies and monomeric or oligomeric Aß species during the dynamic Aß aggregation process. Here, we present a high-resolution native ion-mobility mass spectrometry (nIM-MS) method to investigate complexes formed between a variety of Aß oligomers and three Aß-specific IgGs, namely two antibodies with relatively high conformational specificity (aducanumab and A34) and one antibody with low conformational specificity (crenezumab). We found that crenezumab primarily binds Aß monomers, while aducanumab preferentially binds Aß monomers and dimers and A34 preferentially binds Aß dimers, trimers, and tetrameters. Through collision induced unfolding (CIU) analysis, our data indicate that antibody stability is increased upon Aß binding and, surprisingly, this stabilization involves the Fc region. Together, we conclude that nIM-MS and CIU enable the identification of Aß antibody binding stoichiometries and provide important details regarding antibody binding mechanisms.

Insights into modifiers effects in differential mobility spectrometry: A data science approach for metabolomics and peptidomics.

Utilizing a data-driven approach, this study investigates modifier effects on compensation voltage in differential mobility spectrometry-mass spectrometry (DMS-MS) for metabolites and peptides. Our analysis uncovers specific factors causing signal suppression in small molecules and pinpoints both signal suppression mechanisms and the analytes involved. In peptides, machine learning models discern a relationship between molecular weight, topological polar surface area, peptide charge, and proton transfer-induced signal suppression. The models exhibit robust performance, offering valuable insights for the application of DMS to metabolites and tryptic peptides analysis by DMS-MS.

Faecal Volatile Organic Compound Analysis in De Novo Paediatric Inflammatory Bowel Disease by Gas Chromatography-Ion Mobility Spectrometry: A Case-Control Study.

The gut microbiota and its related metabolites differ between inflammatory bowel disease (IBD) patients and healthy controls. In this study, we compared faecal volatile organic compound (VOC) patterns of paediatric IBD patients and controls with gastrointestinal symptoms (CGIs). Additionally, we aimed to assess if baseline VOC profiles could predict treatment response in paediatric IBD patients. We collected faecal samples from a cohort of de novo therapy-naïve paediatric IBD patients and CGIs. VOCs were analysed using gas chromatography-ion mobility spectrometry (GC-IMS). Response was defined as a combination of clinical response based on disease activity scores, without requiring treatment escalation. We included 109 paediatric IBD patients and 75 CGIs, aged 4 to 17 years. Faecal VOC profiles of paediatric IBD patients were distinguishable from those of CGIs (AUC ± 95% CI, p-values: 0.71 (0.64-0.79), <0.001). This discrimination was observed in both Crohn's disease (CD) (0.75 (0.67-0.84), <0.001) and ulcerative colitis (UC) (0.67 (0.56-0.78), 0.01) patients. VOC profiles between CD and UC patients were not distinguishable (0.57 (0.45-0.69), 0.87). Baseline VOC profiles of responders did not differ from non-responders (0.70 (0.58-0.83), 0.1). In conclusion, faecal VOC profiles of paediatric IBD patients differ significantly from those of CGIs.

Towards optimizing the protocol for untargeted profiling of urine volatiles via gas chromatography-ion mobility spectrometry. A pilot study.

The analysis of volatile organic compounds (VOCs) present in various biological samples holds immense potential for non-invasive disease diagnostics and metabolic profiling. One of the biological fluids that are suitable for use in clinical practice is urine. Given the limited quantity of VOCs in the urine headspace, it's imperative to enhance their extraction into the gaseous phase and prevent any degradation of VOCs during the thawing process. The study aimed to test several key parameters (incubation time, temperature, and thawing) that can influence urine volatilome and monitor selected VOCs for their stability. The analysis in this study was performed using a BreathSpec® (G.A.S., Dortmund, Germany) device consisting of a gas chromatograph (GC) coupled with an ion mobility spectrometer (IMS). Testing three different temperatures and incubation times yielded a low number of VOCs (9 out of 34) that exhibited statistically significant differences. However, examining three thawing conditions revealed no VOCs with statistically significant changes. Thus, we conclude that urine composition remains relatively stable despite exposure to various thermal stresses.

MobiLipid: A Tool for Enhancing CCS Quality Control of Ion Mobility-Mass Spectrometry Lipidomics by Internal Standardization.

Ion mobility-mass spectrometry (IM-MS) offers benefits for lipidomics by obtaining IM-derived collision cross sections (CCS), a conditional property of an ion that can enhance lipid identification. While drift tube (DT) IM-MS retains a direct link to the primary experimental method to derive CCS values, other IM technologies rely solely on external CCS calibration, posing challenges due to dissimilar chemical properties between lipids and calibrants. To address this, we introduce MobiLipid, a novel tool facilitating the CCS quality control of IM-MS lipidomics workflows by internal standardization. MobiLipid utilizes a newly established DTCCSN2 library for uniformly (U)13C-labeled lipids, derived from a U13C-labeled yeast extract, containing 377 DTCCSN2 values. This automated open-source R Markdown tool enables internal monitoring and straightforward compensation for CCSN2 biases. It supports lipid class- and adduct-specific CCS corrections, requiring only three U13C-labeled lipids per lipid class-adduct combination across 10 lipid classes without requiring additional external measurements. The applicability of MobiLipid is demonstrated for trapped IM (TIM)-MS measurements of an unlabeled yeast extract spiked with U13C-labeled lipids. Monitoring the CCSN2 biases of TIMCCSN2 values compared to DTCCSN2 library entries utilizing MobiLipid resulted in mean absolute biases of 0.78% and 0.33% in positive and negative ionization mode, respectively. By applying the CCS correction integrated into the tool for the exemplary data set, the mean absolute CCSN2 biases of 10 lipid classes could be reduced to approximately 0%.

Discrimination and screening of volatile metabolites in atractylodis rhizoma from different varieties using headspace solid-phase microextraction-gas chromatography-mass spectrometry and headspace gas chromatography-ion mobility spectrometry, and ultra-fast gas chromatography electronic nose.

Atractylodis rhizoma is a common bulk medicinal material with multiple species. Although different varieties of atractylodis rhizoma exhibit variations in their chemical constituents and pharmacological activities, they have not been adequately distinguished due to their similar morphological features. Hence, the purpose of this research is to analyze and characterize the volatile organic compounds (VOCs) in samples of atractylodis rhizoma using multiple techniques and to identify the key differential VOCs among different varieties of atractylodis rhizoma for effective discrimination. The identification of VOCs was carried out using headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) and headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS), resulting in the identification of 60 and 53 VOCs, respectively. The orthogonal partial least squares discriminant analysis (OPLS-DA) model was employed to screen potential biomarkers and based on the variable importance in projection (VIP ≥ 1.2), 24 VOCs were identified as critical differential compounds. Random forest (RF), K-nearest neighbor (KNN) and back propagation neural network based on genetic algorithm (GA-BPNN) models based on potential volatile markers realized the greater than 90 % discriminant accuracies, which indicates that the obtained key differential VOCs are reliable. At the same time, the aroma characteristics of atractylodis rhizoma were also analyzed by ultra-fast gas chromatography electronic nose (Ultra-fast GC E-nose). This study indicated that the integration of HS-SPME-GC-MS, HS-GC-IMS and ultra-fast GC E-nose with chemometrics can comprehensively reflect the differences of VOCs in atractylodis rhizoma samples from different varieties, which will be a prospective tool for variety discrimination of atractylodis rhizoma.

Serum untargeted lipidomic characterization in a general Chinese cohort with residual per-/polyfluoroalkyl substances by liquid chromatography-drift tube ion mobility-mass spectrometry.

Per- and polyfluoroalkyl substances (PFAS) remain controversial due to their high persistency and potential human toxicity. Although occupational exposure to PFAS has been widely investigated, the implications of PFAS occurrence in the general population remain to be unraveled. Considering that serum from most people contains PFAS, the aim of this study was to characterize the lipidomic profile in human serum from a general cohort (n = 40) with residual PFAS levels. The geometric means of ∑PFAS (11.8 and 4.4 ng/mL) showed significant differences (p < 0.05) for the samples with the highest (n = 20) and lowest (n = 20) concentrations from the general population respectively. Reverse-phase liquid chromatography coupled to drift tube ion mobility and high-resolution mass spectrometry using dual polarity ionization was used to characterize the lipid profile in both groups. The structural elucidation involved the integration of various parameters, such as retention time, mass-to-charge ratio, tandem mass spectra and collision cross section values. This approach yielded a total of 20 potential biomarkers linked to the perturbed glycerophospholipid metabolism, energy metabolism and sphingolipid metabolism. Among these alterations, most lipids were down-regulated and some specific lipids (PC 36:5, PC 37:4 and PI O-34:2) exhibited a relatively strong Spearman correlation and predictive capacity for PFAS contamination. This study could support further toxicological assessments and mechanistic investigations into the effects of PFAS exposure on the lipidome.

Aza-Prilezhaev Aziridination-Enabled Multidimensional Analysis of Isomeric Lipids via High-Resolution U-Shaped Mobility Analyzer-Mass Spectrometry.

Unsaturated lipids constitute a significant portion of the lipidome, serving as players of multifaceted functions involving cellular signaling, membrane structure, and bioenergetics. While derivatization-assisted liquid chromatography tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidome, it mainly faces challenges in efficiently labeling the carbon-carbon double bond (C═C) and differentiating isomeric lipids in full dimension. This presents a need for new orthogonal methodologies. Herein, a metal- and additive-free aza-Prilezhaev aziridination (APA)-enabled ion mobility mass spectrometric method is developed for probing multiple levels of unsaturated lipid isomerization with high sensitivity. Both unsaturated polar and nonpolar lipids can be efficiently labeled in the form of N-H aziridine without significant side reactions. The signal intensity can be increased by up to 3 orders of magnitude, achieving the nM detection limit. Abundant site-specific fragmentation ions indicate C═C location and sn-position in MS/MS spectra. Better yet, a stable monoaziridination product is dominant, simplifying the spectrum for lipids with multiple double bonds. Coupled with a U-shaped mobility analyzer, identification of geometric isomers and separation of different lipid classes can be achieved. Additionally, a unique pseudo MS3 mode with UMA-QTOF MS boosts the sensitivity for generating diagnostic fragments. Overall, the current method provides a comprehensive solution for deep-profiling lipidomics, which is valuable for lipid marker discovery in disease monitoring and diagnosis.

Innovative direct introduction-ion mobility-mass spectrometry (DI-IM-MS) approach for fast and robust isomer-specific quantification in a complex matrix: Application to 2'-fucosyllactose (2'-FL) in breast milk.

Identification and specific quantification of isomers in a complex biological matrix by mass spectrometry alone is not an easy task due to their identical chemical formula and therefore their same mass-to-charge ratio (m/z). Here, the potential of direct introduction combined with ion mobility-mass spectrometry (DI-IM-MS) for rapid quantification of isomers as human milk oligosaccharides (HMOs) was investigated. Differences in HMO profiles between various analyzed breast milk samples were highlighted using the single ion mobility monitoring (SIM2) acquisition for high ion mobility resolution detection. Furthermore, the Se+ (secretor) or Se- (non-secretor) phenotype could be assigned to breast milk samples studied based on their HMO contents, especially on the response of 2'-fucosyllactose (2'-FL) and lacto-N-fucopentaose I (LNFP I). The possibility of quantifying a specific isomer in breast milk by DI-IM-MS was also investigated. The standard addition method allowed the determination of the 2'-FL despite the presence of other oligosaccharides, including 3-fucosyllactose (3-FL) isomer in breast milk. This proof-of-concept study demonstrated the high potential of such an approach for the rapid and convenient quantification of isomers in complex mixtures.

Theoretical and experimental study on the effect of scanning speed on FAIMS peaks.

High-Field Asymmetric Ion Mobility Spectrometry (FAIMS) is a technique for ion separation and detection based on ion mobility variation under high electronic field. While compensation voltage scanning speed is a fundamental parameter in FAIMS, its impact on spectra remains unclear. In this work, a function referred to as F-EMG is introduced to describe the impact of compensation voltage scanning speed on FAIMS spectra, and the properties of the function are studied. Theoretical analysis emphasizes the impact of the scanning speed on peak height, position, and symmetry, as well as the capability of the F-EMG function to progressively approach Gaussian function at lower scanning speeds. Furthermore, the function indicates that spectra obtained in positive and negative scanning modes exhibits symmetry. An experimental validation, conducted with a custom FAIMS setup and analyzing hydrogen sulfide, ethylbenzene, toluene, styrene, benzene and ammonia, confirms the model's influence on peak features, fitting accuracy, and exhibits a closer alignment with the Gaussian function at lower scanning speeds. Additionally, the experimental data indicate that the spectra show symmetry in positive and negative scanning models. This work not only improves understanding of FAIMS spectral analysis but also introduces a robust method for enhancing data accuracy across varying scanning speeds.

Analysis of Volatile Aroma Components in Different Parts of Shiitake Mushroom (Lentinus edodes) Treated with Ultraviolet C Light-Emitting Diodes Based on Gas Chromatography-Ion Mobility Spectroscopy.

Further assessment of ultraviolet C light-emitting diode (UVC-LED) irradiation for influencing shiitake mushrooms' (Lentinus edodes) volatile and sensory properties is needed. In this study, a comparison of UVC-LED irradiation treatment on the flavor profiles in various parts of shiitake mushrooms was conducted using gas chromatography-ion mobility spectrometry (GC-IMS) and sensory analysis. Sixty-three volatile compounds were identified in shiitake mushrooms. The fresh shiitake mushrooms were characterized by the highest values of raw mushroom odors. After UVC-LED treatment, the content of C8 alcohols decreased, especially that of 1-octen-3-ol, while the content of aldehydes increased, especially the content of nonanal and decanal. The score of fatty and green odors was enhanced. For fresh samples, the mushroom odors decreased and the mushroom-like odors weakened more sharply when treated in ethanol suspension than when treated with direct irradiation. The fruit odors were enhanced using direct UVC-LED irradiation for fresh mushroom samples and the onion flavor decreased. As for shiitake mushroom powder in ethanol suspension treated with UVC-LED, the sweaty and almond odor scores decreased and the vitamin D2 content in mushroom caps and stems reached 668.79 µg/g (dw) and 399.45 µg/g (dw), respectively. The results obtained from this study demonstrate that UVC-LED treatment produced rich-flavored, quality mushroom products.

Structural Characterization of Disaccharides Using Cyclic Ion Mobility Spectrometry and Monosaccharide Standards.

To understand the mode of action of bioactive oligosaccharides, such as prebiotics, in-depth knowledge about all structural features, including monosaccharide composition, linkage type, and anomeric configuration, is necessary. Current analytical techniques provide limited information about structural features within complex mixtures unless preceded by extensive purification. In this study, we propose an approach employing cyclic ion mobility spectrometry (cIMS) for the in-depth characterization of oligosaccharides, here demonstrated for disaccharides. We were able to separate galactose and glucose anomers by exploiting the high ion mobility resolution of cIMS. Using the obtained monosaccharide mobilograms as references, we determined the composition and anomeric configuration of 4ß-galactobiose by studying the monosaccharide fragments generated by collision-induced dissociation (CID) before the ion mobility separation. Drift times and individual MS2 spectra of partially resolved reducing-end anomers of 4ß-galactobiose, 4ß-galactosylglucose (lactose), and 4ß-glucosylglucose (cellobiose) were obtained by deconvolution using CID fragmentation induced in the transfer region between the cIMS cell and TOF analyzer. The composition and anomeric configuration of the reducing end anomers of these disaccharides were identified using cIMS2 approaches, where first each anomer was isolated using cIMS and individually fragmented, and the monosaccharide fragments were again separated by cIMS for comparison with monosaccharide standards. With these results we demonstrate the promising application of cIMS for the structural characterization of isomeric oligosaccharides.

Perspective: The complex relationship between charge, mobility, and gas-phase protein structure.

Ion mobility spectrometry coupled to mass spectrometry (IMS/MS) is a widely used tool for biomolecular separations and structural elucidation. The application of IMS/MS has resulted in exciting developments in structural proteomics and genomics. This perspective gives a brief background of the field, addresses some of the important issues in making structural measurements, and introduces complementary techniques.

Investigating direct current potentials that affect native protein conformation during trapped ion mobility spectrometry-mass spectrometry.

Trapped ion mobility spectrometry-time-of-flight mass spectrometry (TIMS-TOFMS) has emerged as a tool to study protein conformational states. In TIMS, gas-phase ions are guided across the IM stages by applying direct current (DC) potentials (D1-6), which, however, might induce changes in protein structures through collisional activation. To define conditions for native protein analysis, we evaluated the influence of these DC potentials using the metalloenzyme bovine carbonic anhydrase (BCA) as primary test compound. The variation of DC potentials did not change BCA-ion charge and heme content but affected (relative) charge-state intensities and adduct retention. Constructed extracted-ion mobilograms and corresponding collisional cross-section (CCS) profiles gave useful insights in (alterations of) protein conformational state. For BCA, the D3 and D6 potential (which are applied between the deflection transfer and funnel 1 [F1] and the accumulation exit and the start of the ramp, respectively) had most profound effects, showing multimodal CCS distributions at higher potentials indicating gradual unfolding. The other DC potentials only marginally altered the CCS profiles of BCA. To allow for more general conclusions, five additional proteins of diverse molecular weight and conformational stability were analyzed, and for the main protein charge states, CCS profiles were constructed. Principal component analysis (PCA) of the obtained data showed that D1 and D3 exhibit the highest degree of correlation with the ratio of folded and unfolded protein (F/U) as extracted from the mobilograms obtained per set D potential. The correlation of D6 with F/U and protein charge were similar, and D2, D4, and D5 showed an inverse correlation with F/U but were correlated with protein charge. Although DC boundary values for induced conformational changes appeared protein dependent, a set of DC values could be determined, which assured native analysis of most proteins.

Structural Insights into Linkage-Specific Ubiquitin Chains Using Ion Mobility Mass Spectrometry.

The structural characterization and differentiation of four types of oligoubiquitin conjugates [linear (Met1)-, Lys11-, Lys48-, Lys63-linked di-, tri-, and tetraubiquitin chains] using ion mobility mass spectrometry are reported. A comparison of collision cross sections for the same linkage of di-, tri-, and tetraubiquitin chains shows differences in conformational elongation for higher charge states due to the interplay of linkage-derived structure and Coulombic repulsion. For di- and triubiquitin chains, this elongation results in a single narrow feature representing an elongated conformation type for multiple higher charge state species. In contrast, higher charge state tetraubiquitin species do not form a single conformer type as readily. A comparison of different linkages in tetraubiquitin chains reveals greater similarity in conformation type at lower charge states; with increasing charge state, the four linkage types diverge in the relative proportions of elongated conformer types with Met1- ≥ Lys11- > Lys63- > Lys48-linkage. These differences in conformational trends could be discussed with respect to biological functions of linkage-specific polyubiquitinated proteins.

VOC-based detection of prostate cancer using an electronic nose and ion mobility spectrometry: A novel urine-based approach.

BACKGROUND: Many diseases leave behind specific metabolites which can be detected from breath and urine as volatile organic compounds (VOC). Our group previously described VOC-based methods for the detection of bladder cancer and urinary tract infections. This study investigated whether prostate cancer can be diagnosed from VOCs in urine headspace. METHODS: For this pilot study, mid-stream urine samples were collected from 56 patients with histologically confirmed prostate cancer. A control group was formed with 53 healthy male volunteers matched for age who had recently undergone a negative screening by prostate-specific antigen (PSA) and digital rectal exam. Headspace measurements were performed with the electronic nose Cyranose 320TM. Statistical comparison was performed using principal component analysis, calculating Mahalanobis distance, and linear discriminant analysis. Further measurements were carried out with ion mobility spectrometry (IMS) to compare detection accuracy and to identify potential individual analytes. Bonferroni correction was applied for multiple testing. RESULTS: The electronic nose yielded a sensitivity of 77% and specificity of 62%. Mahalanobis distance was 0.964, which is indicative of limited group separation. IMS identified a total of 38 individual analytical peaks, two of which showed significant differences between groups (p < 0.05). To discriminate between tumor and controls, a decision tree with nine steps was generated. This model led to a sensitivity of 98% and specificity of 100%. CONCLUSIONS: VOC-based detection of prostate cancer seems feasible in principle. While the first results with an electronic nose show some limitations, the approach can compete with other urine-based marker systems. However, it seems less reliable than PSA testing. IMS is more accurate than the electronic nose with promising sensitivity and specificity, which warrants further research. The individual relevant metabolites identified by IMS should further be characterized using gas chromatography/mass spectrometry to facilitate potential targeted rapid testing.

Identification of Unique Fragmentation Patterns of Fentanyl Analog Protomers Using Structures for Lossless Ion Manipulations Ion Mobility-Orbitrap Mass Spectrometry.

The opioid crisis in the United States is being fueled by the rapid emergence of new fentanyl analogs and precursors that can elude traditional library-based screening methods, which require data from known reference compounds. Since reference compounds are unavailable for new fentanyl analogs, we examined if fentanyls (fentanyl + fentanyl analogs) could be identified in a reference-free manner using a combination of electrospray ionization (ESI), high-resolution ion mobility (IM) spectrometry, high-resolution mass spectrometry (MS), and higher-energy collision-induced dissociation (MS/MS). We analyzed a mixture containing nine fentanyls and W-15 (a structurally similar molecule) and found that the protonated forms of all fentanyls exhibited two baseline-separated IM distributions that produced different MS/MS patterns. Upon fragmentation, both IM distributions of all fentanyls produced two high intensity fragments, resulting from amine site cleavages. The higher mobility distributions of all fentanyls also produced several low intensity fragments, but surprisingly, these same fragments exhibited much greater intensities in the lower mobility distributions. This observation demonstrates that many fragments of fentanyls predominantly originate from one of two different gas-phase structures (suggestive of protomers). Furthermore, increasing the water concentration in the ESI solution increased the intensity of the lower mobility distribution relative to the higher mobility distribution, which further supports that fentanyls exist as two gas-phase protomers. Our observations on the IM and MS/MS properties of fentanyls can be exploited to positively differentiate fentanyls from other compounds without requiring reference libraries and will hopefully assist first responders and law enforcement in combating new and emerging fentanyls.

Geographical discrimination of Paw San rice cultivated in different regions of Myanmar using near-infrared spectroscopy, headspace-gas chromatography-ion mobility spectrometry and chemometrics.

Paw San rice, also known as "Myanmar pearl rice", is considered the highest quality rice in Myanmar. There are considerable differences in terms of the premium commercial value of Paw San rice, which is an incentive for fraud, e.g. adulteration with cheaper rice varieties or mislabelling its geographical origin. Shwe Bo District is one of the most popular rice growing areas in the Sagaing region of Myanmar which produces the most valued and highly priced Paw San rice (Shwe Bo Paw San). The verification of the geographical origin of Paw San rice is not readily undertaken in the rice supply chain because the existing analytical approaches are time-consuming and expensive. Therefore, there is a need for rapid, robust and cost-effective analytical techniques for monitoring the authenticity and geographical origin of Paw San rice. In this 4-year study, two rapid screening techniques, Fourier-transform near-infrared (FT-NIR) spectroscopy and headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), coupled with chemometric modelling, were applied and compared for the regional differentiation of Paw San rice. In addition, low-level fusion of the FT-NIR and HS-GC-IMS data was performed and its effect on the discriminative power of the chemometric models was assessed. Extensive model validation, including the validation using independent samples from a different production year, was performed. Furthermore, the effect of the sample preparation technique (grinding versus no sample preparation) on the performance of the discriminative model, obtained with FT-NIR spectral data, was assessed. The study discusses the suitability of FT-NIR spectroscopy, HS-GC-IMS and the combination of both approaches for rapid determination of the geographical origin of Paw San rice. The results demonstrated the excellent potential of the FT-NIR spectroscopy as well as HS-GC-IMS for the differentiation of Paw San rice cultivated in two distinct geographical regions. The OPLS-DA model, built using FT-NIR data of rice from 3 production years, achieved 96.67% total correct classification rate of an independent dataset from the 4th production year. The DD-SIMCA model, built using FT-NIR data of ground rice, also demonstrated the highest performance: 94% sensitivity and 97% specificity. This study has demonstrated that FT-NIR spectroscopy can be used as an accessible, rapid and cost-effective screening tool to discriminate between Paw San rice cultivated in the Shwe Bo and Ayeyarwady regions of Myanmar.

Nontargeted Volatile Metabolite Screening and Microbial Contamination Detection in Fermentation Processes by Headspace GC-IMS.

Gas chromatography combined with ion mobility spectrometry (GC-IMS) is a powerful separation and detection technique for volatile organic compounds (VOC). This combination is characterized by exceptionally low detection limits in the low ppbv range, high 2-dimensional selectivity, and robust operation. These qualities make it an ideal tool for nontarget screening approaches. Fermentation broths contain a substantial number of VOC, either from the medium or produced by microbial metabolism, that are currently not regularly measured for process monitoring. In this study, Escherichia coli, Saccharomyces cerevisiae, Levilactobacillus brevis, and Pseudomonas fluorescens were exemplarily used as model organisms and cultivated, and the headspace was analyzed by GC-IMS. Additionally, mixed cultures for every combination of two of the microorganisms were also characterized. Multivariate data analysis of the GC-IMS data revealed that it is possible to differentiate between the microorganisms using PLS-DA with a prediction accuracy of 0.92. The mixed cultures could be separated from the pure cultures with accuracies between 0.87 and 1.00 depending on the organism. GC-IMS data correlate with the optical density and can be used to follow and model growth curves. The root mean squared errors ranged between 10 and 20% of the maximum value, depending on the organism. Peak identification with reference compounds did not reveal specific marker compounds, rather the pattern was found to be responsible for the model performance.

Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data.

The rotationally averaged collision cross-section (CCS) determined by ion mobility-mass spectrometry (IM-MS) facilitates the identification of various biomolecules. Although machine learning (ML) models have recently emerged as a highly accurate approach for predicting CCS values, they rely on large data sets from various instruments, calibrants, and setups, which can introduce additional errors. In this study, we identified and validated that ion's polarizability and mass-to-charge ratio (m/z) have the most significant predictive power for traveling-wave IM CCS values in relation to other physicochemical properties of ions. Constructed solely based on these two physicochemical properties, our CCS prediction approach demonstrated high accuracy (mean relative error of <3.0%) even when trained with limited data (15 CCS values). Given its ability to excel with limited data, our approach harbors immense potential for constructing a precisely predicted CCS database tailored to each distinct experimental setup. A Python script for CCS prediction using our approach is freely available at https://github.com/MSBSiriraj/SVR_CCSPrediction under the GNU General Public License (GPL) version 3.