CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics.

Two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) provides a large amount of molecular information from biological samples. However, the lack of a comprehensive compound library or customizable bioinformatics tool is currently a challenge in GC × GC-TOFMS data analysis. We present an open-source deep learning (DL) software called contour regions of interest (ROI) identification, simulation and untargeted metabolomics profiler (CRISP). CRISP integrates multiple customizable deep neural network architectures for assisting the semi-automated identification of ROIs, contour synthesis, resolution enhancement and classification of GC × GC-TOFMS-based contour images. The approach includes the novel aggregate feature representative contour (AFRC) construction and stacked ROIs. This generates an unbiased contour image dataset that enhances the contrasting characteristics between different test groups and can be suitable for small sample sizes. The utility of the generative models and the accuracy and efficacy of the platform were demonstrated using a dataset of GC × GC-TOFMS contour images from patients with late-stage diabetic nephropathy and healthy control groups. CRISP successfully constructed AFRC images and identified over five ROIs to create a deepstacked dataset. The high fidelity, 512 × 512-pixels generative model was trained as a generator with a Fréchet inception distance of <47.00. The trained classifier achieved an AUROC of >0.96 and a classification accuracy of >95.00% for datasets with and without column bleed. Overall, CRISP demonstrates good potential as a DL-based approach for the rapid analysis of 4-D GC × GC-TOFMS untargeted metabolite profiles by directly implementing contour images. CRISP is available at https://github.com/vivekmathema/GCxGC-CRISP.

Evaluation of normalization strategies for GC-based metabolomics.

INTRODUCTION: For many samples studied by GC-based metabolomics applications, extensive sample preparation involving extraction followed by a two-step derivatization procedure of methoximation and trimethylsilylation (TMS) is typically required to expand the metabolome coverage. Performing normalization is critical to correct for variations present in samples and any biases added during the sample preparation steps and analytical runs. Addressing the totality of variations with an adequate normalization method increases the reliability of the downstream data analysis and interpretation of the results. OBJECTIVES: Normalizing to sample mass is one of the most commonly employed strategies, while the total peak area (TPA) as a normalization factor is also frequently used as a post-acquisition technique. Here, we present a new normalization approach, total derivatized peak area (TDPA), where data are normalized to the intensity of all derivatized compounds. TDPA relies on the benefits of silylation as a universal derivatization method for GC-based metabolomics studies. METHODS: Two sample classes consisting of systematically incremented sample mass were simulated, with the only difference between the groups being the added amino acid concentrations. The samples were TMS derivatized and analyzed using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC-TOFMS). The performance of five normalization strategies (no normalization, normalized to sample mass, TPA, total useful peak area (TUPA), and TDPA) were evaluated on the acquired data. RESULTS: Of the five normalization techniques compared, TUPA and TDPA were the most effective. On PCA score space, they offered a clear separation between the two classes. CONCLUSION: TUPA and TDPA carry different strengths: TUPA requires peak alignment across all samples, which depends upon the completion of the study, while TDPA is free from the requirement of alignment. The findings of the study would enhance the convenient and effective use of data normalization strategies and contribute to overcoming the data normalization challenges that currently exist in the metabolomics community.

GC × GC-HRMS with complementary ionization methods in the suspect screening analysis of fragrance allergens: overwhelming or justified?

Modern gas chromatography-mass spectrometry (GC-MS) allows for the analysis of complex samples, such as fragrances. However, identifying all the constituents in natural fragrance mixtures, especially allergens that need to be listed on product labels, is a significant challenge. This is primarily due to the high complexity of the sample and the fact that electron ionization, the most commonly used ionization method in GC-MS, produces numerous nonspecific fragment ions, often resulting in the absence or very low abundance of the molecular ion. These factors affect confidence in assigning the analyte. In this study, we demonstrate that the combination of GC × GC separation, with high mass resolution and accurate mass measurements, as well as chemical ionization in addition to traditional electron ionization, becomes an efficient tool for reliable qualitative analysis of a mixture containing 100 fragrance allergens, even when many of them are closely related species or isomers. The proposed approach expands the applicability of the comprehensive GC × GC-HRMS method, which includes complementary ionization techniques, from studies on anthropogenic priority pollutants and emerging contaminants to the analysis of natural products. Although targeted qualitative and quantitative analysis of allergens in the modern laboratories is well organized, GC × GC-HRMS, being a useful complement to routine quality control of volatile allergens in fragrances, definitely gives an additional contribution to the analytical cases when conventional 1D-GC-MS faces some problems or uncertainties.

Solid-phase microextraction coupled to comprehensive multidimensional gas chromatography for food analysis.

Solid-phase microextraction and comprehensive multidimensional gas chromatography represent two milestone innovations that occurred in the field of separation science in the 1990s. They have a common root in their introduction and have found a perfect coupling in their evolution and applications. This review will focus on food analysis, where the paradigm has changed significantly over time, moving from a targeted analysis, focusing on a limited number of analytes at the time, to a more holistic approach for assessing quality in a larger sense. Indeed, not only some major markers or contaminants are considered, but a large variety of compounds and their possible interaction, giving rise to the field of foodomics. In order to obtain such detailed information and to answer more sophisticated questions related to food quality and authenticity, the use of SPME-GC × GC-MS has become essential for the comprehensive analysis of volatile and semi-volatile analytes. This article provides a critical review of the various applications of SPME-GC × GC in food analysis, emphasizing the crucial role this coupling plays in this field. Additionally, this review dwells on the importance of appropriate data treatment to fully harness the results obtained to draw accurate and meaningful conclusions.

The influence of drying and storage conditions on the volatilome and cannabinoid content of Cannabis sativa L. inflorescences.

The increasing interest in hemp and cannabis poses new questions about the influence of drying and storage conditions on the overall aroma and cannabinoids profile of these products. Cannabis inflorescences are subjected to drying shortly after harvest and then to storage in different containers. These steps may cause a process of rapid deterioration with consequent changes in precious secondary metabolite content, negatively impacting on the product quality and potency. In this context, in this work, the investigation of the effects of freeze vs tray drying and three storage conditions on the preservation of cannabis compounds has been performed. A multi-trait approach, combining both solid-phase microextraction (SPME) two-dimensional gas chromatography coupled to mass spectrometry (SPME-GC × GC-MS) and high-performance liquid chromatography (HPLC), is presented for the first time. This approach has permitted to obtain the detailed characterisation of the whole cannabis matrix in terms of volatile compounds and cannabinoids. Moreover, multivariate statistical analyses were performed on the obtained data, helping to show that freeze drying conditions is useful to preserve cannabinoid content, preventing decarboxylation of acid cannabinoids, but leads to a loss of volatile compounds which are responsible for the cannabis aroma. Furthermore, among storage conditions, storage in glass bottle seems more beneficial for the retention of the initial VOC profile compared to open to air dry tray and closed high-density polyethylene box. However, the glass bottle storage condition causes formation of neutral cannabinoids at the expenses of the highly priced acid forms. This work will contribute to help define optimal storage conditions useful to produce highly valuable and high-quality products.

Applying a risk assessment guided evaluation for verifying comprehensive two-dimensional gas chromatography to analyse complex pharmaceuticals.

The reliability of analytical results is critical and indispensable when applied in regulated environments such as the pharmaceutical industry. Therefore, analytical workflows must be validated. However, validation guidelines are often designed for quantitative targeted analysis and rarely apply to qualitative untargeted approaches. In this study, we employ a risk assessment approach to identify critical parameters which might influence the qualitative results derived by online derivatisation - comprehensive two-dimensional gas chromatography coupled to a high-resolution time-of-flight mass spectrometer (GC × GC-HR-ToF-MS) for the analysis of the active pharmaceutical ingredient (API) sodium bituminosulfonate (SBS). To show the complexity and feasibility of such an approach, we focus on investigating three potential risk factors: sample preparation, vapourability, and the thermal stability of sulfonates. Through the individual evaluation of these potential risk factors due to the application of sample preparation approaches and thermal gravimetric analysis (TGA), we demonstrate the high derivatisation efficiency and repeatability of the online derivatisation method and confirm the absence of derivatisation-induced side reactions. In addition, we also show the potential thermal instability of an incompletely derivatised API. To address the limitation of these individual assessments, we applied a holistic evaluation step with negative electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI( -) FT-ICR MS) as an orthogonal technique. This confirms that most of the API is detected via the presented GC-based method. Thereby, we demonstrated the practical feasibility of the risk assessment-based approach to ensure the validity of the qualitative data for a complex untargeted method.

Comprehensive Two-Dimensional Gas Chromatography with a TOF MS Detector-An Effective Tool to Trace the Signature of Grape Varieties.

Varietal volatile compounds are characteristic of each variety of grapes and come from the skins of the grapes. This work focuses on the development of a methodology for the analysis of free compounds in grapes from Trincadeira, Cabernet Sauvignon, Syrah, Castelão and Tinta Barroca from the 2021 and 2022 harvests, using HS-SPME-GC × GC-TOFMS. To achieve this purpose, a previous optimization step of sample preparation was implemented, with the optimized conditions being 4 g of grapes, 2 g of NaCl, and 2 mL of H2O. The extraction conditions were also optimized, and it was observed that performing the extraction for 40 min at 60 °C was the best for identifying more varietal compounds. The fiber used was a triple fiber of carboxen/divinylbenzene/polydimethylsiloxane (CAR/DVB/PDMS). In addition to the sample preparation, the analytical conditions were also optimized, enabling the adequate separation of analytes. Using the optimized methodology, it was possible to identify fifty-two free volatile compounds, including seventeen monoterpenes, twenty-eight sesquiterpenes, and seven C13-norisoprenoids. It was observed that in 2021, more free varietal volatile compounds were identifiable compared to 2022. According to the results obtained through a linear discriminant analysis (LDA), the differences in volatile varietal signature are observed both among different grape varieties and across different years.

Forensic significance of VOCs profiling in decayed ante- and post-mortem injuries by GC×GC-TOF/MS.

Accurately identifying and differentiating the types of injuries in decomposed corpses is a major challenge in forensic identification. Forensic investigations involving decomposed cadavers pose challenges in determining the cause of death. Traditional methods often lack conclusive evidence. However, the implementation of advanced analytical techniques, such as comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC-TOF/MS), shows promise in overcoming these limitations, but the potential in this area remains limited. Therefore, this study aims to bridge this gap by exploring the potential of GC × GC-TOF/MS in the analysis of volatile organic compounds (VOCs) changes within decaying ante- and post-mortem injuries.The research emphasizes the forensic significance of VOCs changes in decomposed cadavers. We used GC × GC-TOF/MS analysis to identify the specific volatile compounds in putrefied corpse tissue samples from mice. The GC × GC-TOF/MS analysis results showed that under winter conditions, PC1 explained 57.16% of the variance, and PC2 explained 25.23% of the variance; while under summer conditions, PC1 explained 71.89% of the variance, and PC2 explained 24.49% of the variance. This demonstrates the potential of GC × GC-TOF/MS in identifying specific VOCs present in tissue samples that can serve as potential biomarkers for distinguishing between antemortem and postmortem injury. GC × GC-TOF/MS analysis revealed distinct VOC patterns in both conditions. Comprehensive use of GC × GC-TOF/MS analysis enhances accuracy in identifying and characterizing ante- and post-mortem injuries in decomposed cadavers. This study can significantly contribute to the field of forensic medicine and improve the accuracy of forensic investigations.

Optimization of fecal sample homogenization for untargeted metabolomics.

INTRODUCTION: Fecal samples are highly complex and heterogeneous, containing materials at various stages of digestion. The heterogeneity and complexity of feces make stool metabolomics inherently challenging. The level of homogenization influences the outcome of the study, affecting the metabolite profiles and reproducibility; however, there is no consensus on how fecal samples should be prepared to overcome the topographical discrepancy and obtain data representative of the stool as a whole. OBJECTIVES: Various combinations of homogenization conditions were compared to investigate the effects of bead size, addition of solvents and the differences between wet-frozen and lyophilized feces. METHODS: The homogenization parameters were systematically altered to evaluate the solvent usage, bead size, and whether lyophilization is required in homogenization. The metabolic coverage and reproducibility were compared among the different conditions. RESULTS: The current work revealed that a combination of mechanical and chemical lysis obtained by bead-beating with a mixture of big and small sizes of beads in an organic solvent is an effective way to homogenize fecal samples with adequate reproducibility and metabolic coverage. Lyophilization is required when bead-beating is not available. CONCLUSIONS: A comprehensive and systematical evaluation of various fecal matter homogenization conditions provides a profound understanding for the effects of different homogenization methods. Our findings would be beneficial to assist with standardization of fecal sample homogenization protocol.

Distinct emissions of biogenic volatile organic compounds from temperate benthic taxa.

INTRODUCTION: Biogenic volatile organic compounds (BVOCs) are emitted by all organisms as intermediate or end-products of metabolic processes. Individual BVOCs perform important physiological, ecological and climatic functions, and collectively constitute the volatilome-which can be reflective of organism taxonomy and health. Although BVOC emissions of tropical benthic reef taxa have recently been the focus of multiple studies, emissions derived from their temperate counterparts have never been characterised. OBJECTIVES: Characterise the volatilomes of key competitors for benthic space among Australian temperate reefs. METHODS: Six fragments/fronds of a temperate coral (Plesiastrea versipora) and a macroalga (Ecklonia radiata) from a Sydney reef site were placed within modified incubation chambers filled with seawater. Organism-produced BVOCs were captured on thermal desorption tubes using a purge-and-trap methodology, and were then analysed using GC × GC - TOFMS and multivariate tests. RESULTS: Analysis detected 55 and 63 BVOCs from P. versipora and E. radiata respectively, with 30 of these common between species. Each taxon was characterised by a similar relative composition of chemical classes within their volatilomes. However, 14 and 10 volatiles were distinctly emitted by either E. radiata or P. versipora respectively, including the halogenated compounds iodomethane, tribromomethane, carbon tetrachloride and trichloromonofluoromethane. While macroalgal cover was 3.7 times greater than coral cover at the sampling site, P. versipora produced on average 17 times more BVOCs per cm2 of live tissue, resulting in an estimated contribution to local BVOC emission that was 4.7 times higher than E. radiata. CONCLUSION: Shifts in benthic community composition could disproportionately impact local marine chemistry and affect how ecosystems contribute to broader BVOC emissions.

Correlations for untargeted GC × GC-HRTOF-MS metabolomics of colorectal cancer.

INTRODUCTION: Modern comprehensive instrumentations provide an unprecedented coverage of complex matrices in the form of high-dimensional, information rich data sets. OBJECTIVES: In addition to the usual biomarker research that focuses on the detection of the studied condition, we aimed to define a proper strategy to conduct a correlation analysis on an untargeted colorectal cancer case study with a data set of 102 variables corresponding to metabolites obtained from serum samples analyzed with comprehensive two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry (GC × GC-HRTOF-MS). Indeed, the strength of association existing between the metabolites contains potentially valuable information about the molecular mechanisms involved and the underlying metabolic network associated to a global perturbation, at no additional analytical effort. METHODS: Following Anscombe's quartet, we took particular attention to four main aspects. First, the presence of non-linear relationships through the comparison of parametric and non-parametric correlation coefficients: Pearson's r, Spearman's rho, Kendall's tau and Goodman-Kruskal's gamma. Second, the visual control of the detected associations through scatterplots and their associated regressions and angles. Third, the effect and handling of atypical samples and values. Fourth, the role of the precision of the data on the attribution of the ranks through the presence of ties. RESULTS: Kendall's tau was found the method of choice for the data set at hand. Its application highlighted 17 correlations significantly altered in the active state of colorectal cancer (CRC) in comparison to matched healthy controls (HC), from which 10 were specific to this state in comparison to the remission one (R-CRC) investigated on distinct patients. 15 metabolites involved in the correlations of interest, on the 25 unique ones obtained, were annotated (Metabolomics Standards Initiative level 2). CONCLUSIONS: The metabolites highlighted could be used to better understand the pathology. The systematic investigation of the methodological aspects that we expose allows to implement correlation analysis to various fields and many specific cases.

Comprehensive Two-Dimensional Gas Chromatography with Peak Tracking for Screening of Constituent Biodegradation in Petroleum UVCB Substances.

Petroleum substances, as archetypical UVCBs (substances of unknown or variable composition, complex reaction products, or biological substances), pose a challenge for chemical risk assessment as they contain hundreds to thousands of individual constituents. It is particularly challenging to determine the biodegradability of petroleum substances since each constituent behaves differently. Testing the whole substance provides an average biodegradation, but it would be effectively impossible to obtain all constituents and test them individually. To overcome this challenge, comprehensive two-dimensional gas chromatography (GC × GC) in combination with advanced data-handling algorithms was applied to track and calculate degradation half-times (DT50s) of individual constituents in two dispersed middle distillate gas oils in seawater. By tracking >1000 peaks (representing ∼53-54% of the total mass across the entire chromatographic area), known biodegradation patterns of oil constituents were confirmed and extended to include many hundreds not currently investigated by traditional one-dimensional GC methods. Approximately 95% of the total tracked peak mass biodegraded after 64 days. By tracking the microbial community evolution, a correlation between the presence of functional microbial communities and the observed progression of DT50s between chemical classes was demonstrated. This approach could be used to screen the persistence of GC × GC-amenable constituents of petroleum substance UVCBs.

One-dimensional and comprehensive two-dimensional gas chromatographic approaches for the characterization of post-consumer recycled plastic materials.

In September 2022, the European Commission published its new regulation on recycled plastic materials for food contact. It allows newly developed, non-authorized technologies and approaches, or so-called novel technologies, to be deployed in the field to generate the data needed for establishing regulatory and/or fit for purpose processes. The data shall be generated by using suitable methods, but the regulation does not give a more detailed description on those. In this study, commercially purchased buckets made of post-consumer recycled polypropylene were screened, using a number of different analytical approaches. Sample preparation methods, analysis techniques, and the data and information generated were compared. The results clearly demonstrate the need for a detailed characterization of such materials and the advantages and disadvantages of the analysis using conventional gas chromatography with flame ionization detection and mass spectrometery as well as two-dimensional comprehensive gas chromatography with time of flight mass spectrometry.

Comprehensive two-dimensional gas chromatography-time of flight mass spectrometry as a tool for tracking roasting-induced changes in the volatilome of cold-pressed rapeseed oil.

The aim of this study was to track changes in the volatilome of cold-pressed oil and press cakes obtained from roasted seeds and to combine it with the profile of non-volatile metabolites in a single study, in order to understand pathways of volatile organic compound (VOC) formation caused by thermal processing. Comprehensive two-dimensional gas chromatography-time of flight mass spectrometry was used for the analysis of VOCs in cold-pressed oils and corresponding press cakes obtained after roasting of seeds at 140 and 180 °C prior to pressing. Contents of primary metabolites (amino acids, saccharides, fatty acids) as well as selected secondary metabolites (glucosinolates, polyphenols) were determined, as many of them serve as precursors to volatile compounds formed especially in thermal reactions. After roasting, the formation of Maillard reaction products increased, which corresponded to the reduction of free amino acids and monosaccharides. Moreover, levels of the products of thermal oxidation of fatty acids, such as aldehydes and ketones, increased with the increasing temperature of roasting, although no significant changes were noted for fatty acids. Among sulphur-containing compounds, contents of the products and intermediates of methionine Strecker degradation increased significantly with the increasing temperature of roasting. Degradation of glucosinolates to nitriles occurred after thermal treatment. The results of this study confirmed that seed roasting before cold pressing has a significant effect on the volatiles, but also indicated roasting-induced changes in non-volatile metabolites of oil and press cake. Such an approach helps to understand metabolic changes occurring during rapeseed processing in cold-pressed oil production.

Comprehensive two-dimensional gas chromatography with flow modulator coupled via tube plasma ionization to an atmospheric pressure high-resolution mass spectrometer for the analysis of vermouth volatile profile.

The analysis of complex samples is a big analytical challenge due to the vast number of compounds present in these samples as well as the influence matrix components could cause in the methodology. In this way, comprehensive two-dimensional gas chromatography coupled to mass spectrometry (GC × GC-MS) is a very powerful tool to achieve the characterization of complex samples. Nevertheless, due to possible coelutions occurring in these matrices, mixed spectra are generally obtained with electron ionization (EI) which could extremely complicate the identification of the analytes. Thereby, new methodology setups are required to improve the confidence on the identification in non-targeted determinations. Here, we present a high-throughput methodology consisting of GC × GC with flow modulation coupled to high-resolution atmospheric pressure mass spectrometry (HRMS) via a novel tube plasma ion source (TPI). The flow modulator allows to easily automate the GC × GC method compared to traditional cryo-modulators, while the soft ionization provided by TPI helps to preserve the [M]+• or [M+H]+ ions, thus increasing the confidence in the identification. Additionally, the combination of a flow modulation with an atmospheric pressure mass spectrometer significantly improves the sensitivity over flow modulated GC × GC-EI-MS methods because no split is required. This methodology was applied to the analysis of a complex sample such as vermouth where the volatile profile is usually considered by consumers as a product quality indicator since it raises the first sensations produced during its consumption. Using this approach, different classes of compounds were tentatively identified in the sample, including monoterpenes, terpenoids, sesquiterpenoids and carboxylic acid, and carboxylate esters among others, showing the great potential of a GC × GC-TPI-qTOF-MS platform for improving the confidence of the identifications in non-targeted applications.

Analysis of complex drugs by comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry: detailed chemical description of the active pharmaceutical ingredient sodium bituminosulfonate and its process intermediates.

The European pharmacopeia provides analytical methods for the chemical characterization of active pharmaceutical ingredients (APIs). However, the complexity of some APIs exceeds the limitations of the currently prevailing physicochemical methods. Sodium bituminosulfonate (SBS) is described by the collection of key parameters of generalizing criteria such as dry matter, sulfur and sodium content, and neutrality, but techniques to unravel the complexity on a molecular level are lacking. We present a study based on online derivatization with tetramethylammonium hydroxide in combination with comprehensive two-dimensional gas chromatography coupled to an electron ionization high-resolution time-of-flight mass spectrometer (GC × GC-HR-ToF-MS) for the chemical description of SBS as well as its process intermediates. The application of GC × GC allowed the comprehensive description of the chemical components in the API and the process intermediates for the first time. Furthermore, it was possible to classify peaks regarding their elemental and structural composition based on accurate mass information, elution behavior, and mass fragmentation pattern. This work demonstrates not only the general applicability, advantages but also limitations of GC × GC for the characterization of APIs for complex drugs.

Hyperspeed method for analyzing organochloride pesticides in sediments using two-dimensional gas chromatography-time-of-flight mass spectrometry.

Pesticides are traditionally analyzed using conventional gas chromatography. When fast chromatography is associated with comprehensive two-dimensional gas chromatography (GC × GC), the resulting method presents high-resolution separation associated with a higher chromatographic speed. In the present work, a method for pesticide analysis in sediment samples was developed using quick, easy, cheap, effective, rugged, and safe extraction (QuEChERS) and a hyperspeed GC × GC separation. The QuEChERS procedure reported in the literature was extended to incorporate the analytes tetrachloro-m-xylene, decachlorobiphenyl, trans-chlordane, chlordane, endosulfan lactone, and endosulfan ether. To understand the chromatographic method improvement achieved, the recent concept of average theoretical peak time (ATPT) was used. The ATPT improved from that of the traditional GC × GC separation to the proposed method, and the separation speed can be classified as a hyperspeed separation. The limit of detection and quantitation of the compounds in the standard mix ranged from 0.39 to 17.96 µg L-1 and 1.18 to 54.43 µg L-1, respectively. The method showed acceptable RSD% (relative standard deviation) values and little interference of the sediment matrix in the extraction procedure. The developed method was applied to the determination of a mixture of 19 compounds in 16 sediment samples from the Pirapetinga River and Paraíba do Sul River in Brazil.

DA_2DCHROM - a data alignment tool for applications on real GC × GC-TOF samples.

Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) has great potential for analyses of complicated mixtures and sample matrices, due to its separation power and possible high resolution. The second component of the measurement results, the mass spectra, is reproducible. However, the reproducibility of two-dimensional chromatography is affected by many factors and makes the evaluation of long-term experiments or cross-laboratory collaborations complicated. This paper presents a new open-source data alignment tool to tackle the problem of retention time shifts - with 5 different algorithms implemented: BiPACE 2D, DISCO, MSort, PAM, and TNT-DA, along with Pearson's correlation and dot product as optional methods for mass spectra comparison. The implemented data alignment algorithms and their variations were tested on real samples to demonstrate the functionality of the presented tool. The suitability of each implemented algorithm for significantly/non-significantly shifted data was discussed on the basis of the results obtained. For the evaluation of the "goodness" of the alignment, Kolmogorov-Smirnov test values were calculated, and comparison graphs were generated. The DA_2DChrom is available online with its documentation, fully open-sourced, and the user can use the tool without the need of uploading their data to external third-party servers.

Linking Pedobacter lusitanus NL19 volatile exometabolome with growth medium composition: what can we learn using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry?

Microbial metabolomics allows understanding and to comprehensively analyse metabolites, and their related cellular and metabolic processes, that are produced and released to the extracellular environment under specific conditions. In that regard, the main objective of this research is to understand the impact of culture media changes in the metabolic profile of Pedobacter lusitanus NL19 (NL19) and Pedobacter himalayensis MTCC 6384 (MTCC6384) and respective influence on the production of biotechnologically relevant compounds. Solid-phase microextraction combined with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry with time-of-flight analyser (GC × GC-ToFMS) was applied to comprehensively study the metabolites produced by NL19 and MTCC6384 both in tryptic soy broth 100% (TSB100) and tryptic soy broth with 25% casein peptone (PC25). A total of 320 metabolites were putatively identified, which belong to different chemical families: alcohols, aldehydes, esters, ethers, hydrocarbons, ketones, nitrogen compounds, sulphur compounds, monoterpenes, and sesquiterpenes. Metabolites that were statistically different from the control (sterile medium) were selected allowing for the construction of the metabolic profile of both strains. A set of 80 metabolites was tentatively associated to the metabolic pathways such as the metabolism of fatty acids, branched-chain aminoacids, phenylalanine, methionine, aromatic compounds, and monoterpene and sesquiterpene biosynthesis. This study allowed to better understand how slight changes of the culture media and thus the composition of nutrients impair the metabolic profile of bacteria, which may be further explored for metabolomics pipeline construction or biotechnological applications.

A method for the determination of 70 pesticides in extra virgin olive oil based on a limited-volume solvent extraction step prior to comprehensive two-dimensional gas chromatography-tandem mass spectrometry.

The goal of the present research was to develop a method based on a miniaturized solvent extraction step (using only 500 µL of acetonitrile, with no further clean-up or concentration processes) prior to cryogenic-modulation comprehensive two-dimensional gas chromatography-tandem mass spectrometry for the determination of seventy pesticides in extra virgin olive oil, exploiting the enhanced specificity and sensitivity of this technique. Limits of quantification were always below European legislation residue limits, intra-day precision was between 0.3 and 4.9% (at the 50 and 100 µg kg-1 concentration levels), inter-day precision was between 1.6 and 6.1% (at the 100 µg kg-1 concentration level), recovery (at the 20, 50, and 100 µg kg-1 concentration levels) was in the 14-120% range, accuracy at the initial stage of the work (within repeatability conditions) was between 79 and 110%, while accuracy after 3 months (within intermediate precision conditions) was between 91 and 121% (at the 50 and 100 µg kg-1 concentration levels). Finally, the matrix effect was always positive, between 16 and 197%. The method was applied to the investigation of twenty samples, and eleven of these were found to be contaminated.