bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒07‒09
25 papers selected by
Sofia Costa

  1. Methods Mol Biol. 2023 ;2688 135-146
      Metabolites reflect the biological state of cells and tissue, and metabolomics is therefore a field of high interest both to understand normal physiological functions and disease development. When studying heterogeneous tissue samples, mass spectrometry imaging (MSI) is a valuable tool as it conserves the spatial distribution of analytes on tissue sections. A large proportion of metabolites are, however, small and polar, making them vulnerable to delocalizing through diffusion during sample preparation. Here we present a sample preparation method optimized to limit diffusion and delocalization of small polar metabolites in fresh frozen tissue sections. This sample preparation protocol includes cryosectioning, vacuum frozen storage, and matrix application. The methods described were primely developed for matrix-assisted laser desorption/ionization (MALDI) MSI, but the protocol describing cryosectioning and vacuum freezing storage can also be applied before desorption electrospray ionization (DESI) MSI. Our vacuum drying and vacuum packing approach offers a particular advantage to limit delocalization and safe storage.
    Keywords:  Analyte localization; Cryosectioning; Fresh frozen tissue; Mass spectrometry imaging; Matrix application; Small metabolites
  2. Anal Bioanal Chem. 2023 Jul 03.
      Analyzing the composition of (human) urine plays a major role in the fields of biology and medicine. Organic molecules (such as urea, creatine) and ions (such as chloride, sulfate) are the major compounds present in urine, the quantification of which allows for the diagnosis of a subject's health condition. Various analytical methods have been reported for studying urine components and validated on the basis of known and referenced compounds. The present work introduces a new method able to simultaneously determine both major organic molecules and ions contained in urine, by combining ion chromatography using a conductimetric detector with mass spectroscopy. The analysis of organic and ionized compounds (anionic and cationic) was achieved in double injections. For quantification, the standard addition method was used. Human urine samples were pre-treated (diluted and filtered) for IC-CD/MS analysis. The analytes were separated in 35 min. Calibration ranges (0-20 mg.L-1) and correlation coefficients (> 99.3%) as well as detection (LODs < 0.75 mg.L-1) and quantification (LOQs < 2.59 mg.L-1) limits were obtained for the main organic molecules (lactic, hippuric, citric, uric, oxalic acids, urea, creatine, and creatinine) and ions (chloride, sulfate, phosphate, sodium, ammonium, potassium, calcium, and magnesium) contained in urine. The intra- and inter-day accuracies of the analytes consistently ranged from 0.1 to 5.0%, and the precision was within 4.0%. For all analytes, no significant matrix effects were observed, and recoveries ranged from 94.9 to 102.6%. Finally, quantitative results of analytes were obtained from 10 different human urine samples.
    Keywords:  Human urine analysis; Ion chromatography; Ion exchange; Mass spectrometry; Matrix effect; One-pot quantification
  3. J Am Soc Mass Spectrom. 2023 Jul 07.
      Optimization of mass spectrometric parameters for a data dependent acquisition (DDA) experiment is essential to increase the MS/MS coverage and hence increase metabolite identifications in untargeted metabolomics. We explored the influence of mass spectrometric parameters including mass resolution, radio frequency (RF) level, signal intensity threshold, number of MS/MS events, cycle time, collision energy, maximum ion injection time (MIT), dynamic exclusion, and automatic gain control (AGC) target value on metabolite annotations on an Exploris 480-Orbitrap mass spectrometer. Optimal annotation results were obtained by performing ten data dependent MS/MS scans with a mass isolation window of 2.0 m/z and a minimum signal intensity threshold of 1 × 104 at a mass resolution of 180,000 for MS and 30,000 for MS/MS, while maintaining the RF level at 70%. Furthermore, combining an AGC target value of 5 × 106 and MIT of 100 ms for MS and an AGC target value of 1 × 105 and an MIT of 50 ms for MS/MS scans provided an improved number of annotated metabolites. A 10 s exclusion duration and a two stepped collision energy were optimal for higher spectral quality. These findings confirm that MS parameters do influence metabolomics results, and propose strategies for increasing metabolite coverage in untargeted metabolomics. A limitation of this work is that our parameters were only optimized for one RPLC method on single matrix and may be different for other protocols. Additionally, no metabolites were identified at level 1 confidence. The results presented here are based on metabolite annotations and need to be validated with authentic standards.
    Keywords:  Data dependent acquisition; Mass spectrometric parameters; Optimization; Orbitrap mass spectrometer; Untargeted metabolomics
  4. J Lipid Res. 2023 Jul 03. pii: S0022-2275(23)00082-2. [Epub ahead of print] 100409
      Vitamin D analysis by mass spectrometry faces several analytical challenges, including inefficient ionization of vitamin D compounds, non-specific fragmentation patterns, interferences from epimers, isomers and isobars, as well as very low concentration levels for some of the metabolites in blood samples. Derivatization has been a solution to several of these problems. In this study, we used 2-fluoro-1-methylpyridinium p-toluene sulfonate (FMP-TS) for the first time for derivatization of vitamin D3 metabolites, with the aim of increasing detection sensitivity and allowing for full chromatographic separation of vitamin D isomers and epimers. UHPLC-MS/MS was used for the measurement of five major vitamin D3 metabolites in human serum. Compared to Amplifex and 4-phenyl-1,2,4-triazolin-3,5-dion (PTAD), the FMP-TS reaction required less time to be performed (only 15 min). Multiple experimental conditions of the method were optimized and validated to ensure the accuracy, precision and reliability of the method. In-house and commercially available quality control samples were used to assure the quality of the results for 25-hydroxyvitamin D3. The method showed very good linearity and intra- and inter-day accuracy and precision; coefficients of determination (r2) ranged between 0.9977-0.9992, relative recovery from 95-111% and coefficient of variation from 0.9-11.3. Stability tests showed that the extracted derivatized serum samples were stable for 24 h after storage at -20 oC. Additionally, 24,25(OH)2D3 and 1,25(OH)2D3-FMP derivatives were stable for 1 week when stored at -80 oC. The optimized method was successfully applied to human samples of healthy individuals for quantitative determination of vitamin D3, the two epimers of 25-hydroxyvitamin D3 and 24,25-dihydroxyvitamin D3.
    Keywords:  25-hydroxyvitamin D(3); FMP-TS; LC-MS/MS; Vitamin D(3) metabolites; chemical derivatization
  5. J Chromatogr A. 2023 Jun 22. pii: S0021-9673(23)00399-0. [Epub ahead of print]1705 464173
      Despite the progress in the quantification of xenobiotics, the development and validation of methods designed for endogenous substances still remain challenging due to the natural presence of the analytes in a biological matrix, leading to the inability to obtain a blank sample. Several generally recognized procedures are described to solve this issue, like using surrogate or analyte-depleted matrices or surrogate analytes. However, the workflows used do not always meet the requirements for developing a reliable analytical method or are cost-intensive. This study aimed to design an alternative approach for preparing validation reference samples using authentic analytical standards while preserving the nature of the biological matrix and solving the problem with the inherent presence of analyzed compounds in a studied matrix. The methodology used is based on the standard-addition type procedure. However, unlike the original method, the addition is modified according to a previously measured basal concentration of monitored substances in the pooled biological sample to obtain a predefined concentration in reference samples according to the European Medicines Agency (EMA) validation guideline. The study shows the advantages of described approach on an example of LC-MS/MS analysis of 15 bile acids in human plasma and compares it with other methods commonly used in this field. The method was successfully validated according to the EMA guideline with lower limit of quantification of 5 nmol/L and linearity in the range of 5 - 2000 nmol/L. Finally, the method was used in a metabolomic study on a cohort of pregnant women (n = 28) to confirm intrahepatic cholestasis, the major liver disease observed in pregnancy.
    Keywords:  Alternative validation; Bile acids; LC-MS/MS
  6. Analyst. 2023 Jul 07.
      Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a universal method for the quantitative analysis of small molecular drugs in therapeutic drug monitoring (TDM). Alternatively, liquid chromatography-miniature mass spectrometry (LC-Mini MS) is a simple operating technique for quantitative analysis. However, the wide chromatographic peaks and long retention times of TDM samples using the LC-Mini MS system deteriorated the accuracy and efficiency of quantitative analysis. Here, an optimized electrospray ionization (ESI) interface setup with a splitter valve and a capillary needle (I.D. 30 μm and O.D. 150 μm) of the LC-Mini MS system was acquired. The chromatographic peaks were narrower and smoother and the retention time was shorter for TDM compounds. Furthermore, a quantitative analysis method for risperidone and the active metabolite 9-hydroxyrisperidone in plasma was developed based on this optimal LC-Mini MS setup. The results showed that the calibration curves of risperidone and 9-hydroxyrisperidone had good linear ranges of 2-100 ng mL-1 (R2 = 0.9931) and 2-100 ng mL-1 (R2 = 0.9915), respectively. Finally, the matrix effects, recoveries and stability of risperidone and 9-hydroxyrisperidone samples were analyzed. The results satisfied the requirements of quantitative validation in routine TDM procedures.
  7. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Jun 16. pii: S1570-0232(23)00188-5. [Epub ahead of print]1226 123778
      Different calibration strategies are used in liquid chromatography hyphenated to mass spectrometry (LC-MS) bioanalysis. Currently, the surrogate matrix and surrogate analyte represent the most widely used approaches to compensate for the lack of analyte-free matrices in endogenous compounds quantification. In this context, there is a growing interest in rationalizing and simplifying quantitative analysis using a one-point concentration level of stable isotope-labeled (SIL) standards as surrogate calibrants. Accordingly, an internal calibration (IC) can be applied when the instrument response is translated into analyte concentration via the analyte-to-SIL ratio performed directly in the study sample. Since SILs are generally used as internal standards to normalize variability between authentic study sample matrix and surrogate matrix used for the calibration, IC can be calculated even if the calibration protocol was achieved for an external calibration (EC). In this study, a complete dataset of a published and fully validated method to quantify an extended steroid profile in serum was recomputed by adapting the role of SIL internal standards as surrogate calibrants. Using the validation samples, the quantitative performances for IC were comparable with the original method, showing acceptable trueness (79%-115%) and precision (0.8%-11.8%) for the 21 detected steroids. The IC methodology was then applied to human serum samples (n = 51) from healthy women and women diagnosed with mild hyperandrogenism, showing high agreement (R2 > 0.98) with the concentrations obtained using the conventional quantification based on EC. For IC, Passing-Bablok regression showed proportional biases between -15.0% and 11.3% for all quantified steroids, with an average difference of -5.8% compared to EC. These results highlight the reliability and the advantages of implementing IC in clinical laboratories routine to simplify quantification in LC-MS bioanalysis, especially when a large panel of analytes is monitored.
    Keywords:  External calibration; Internal calibration; LC-MS; Quantification; Steroids
  8. Anal Chem. 2023 Jul 05.
      Direct-infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FTICR MS) shows great promise for metabolomic analysis due to ultrahigh mass accuracy and resolution. However, most of the DI-FTICR MS approaches focused on high-throughput metabolomics analysis at the expense of sensitivity and resolution and the potential for metabolome characterization has not been fully explored. Here, we proposed a novel deep characterization approach of serum metabolome using a segment-optimized spectral-stitching DI-FTICR MS method integrated with high-confidence and database-independent formula assignments. With varied acquisition parameters for each segment, a highly efficient acquisition was achieved for the whole mass range with sub-ppm mass accuracy. In a pooled human serum sample, thousands of features were assigned with unambiguous formulas and possible candidates based on highly accurate mass measurements. Furthermore, a reaction network was used to select confidently unique formulas from possible candidates, which was constructed by unambiguous formulas and possible candidates connected by the formula differences resulting from biochemical and MS transformation. Compared with full-range and conventional segment acquisition, 8- and 1.2-fold increases in observed features were achieved, respectively. Assignment accuracy was 93-94% for both a standard mixture containing 190 metabolites and a spiked serum sample with the root mean square mass error of 0.15-0.16 ppm. In total, 3534 unequivocal neutral molecular formulas were assigned in the pooled serum sample, 35% of which are contained in the HMDB. This method offers great enhancement in the deep characterization of serum metabolome by DI-FTICR MS.
  9. J Chromatogr A. 2023 Jun 19. pii: S0021-9673(23)00398-9. [Epub ahead of print]1705 464172
      Feature extraction is the most fundamental step when analyzing liquid chromatography-mass spectrometry (LC-MS) datasets. However, traditional methods require optimal parameter selections and re-optimization for different datasets, thus hindering efficient and objective large-scale data analysis. Pure ion chromatogram (PIC) is widely used because it avoids the peak splitting problem of the extracted ion chromatogram (EIC) and regions of interest (ROIs). Here, we developed a deep learning-based pure ion chromatogram method (DeepPIC) to find PICs using a customized U-Net from centroid mode data of LC-MS directly and automatically. A model was trained, validated, and tested on the Arabidopsis thaliana dataset with 200 input-label pairs. DeepPIC was integrated into KPIC2. The combination enables the entire processing pipeline from raw data to discriminant models for metabolomics datasets. The KPIC2 with DeepPIC was compared against other competing methods (XCMS, FeatureFinderMetabo, and peakonly) on the MM48, simulated MM48, and quantitative datasets. These comparisons showed that DeepPIC outperforms XCMS, FeatureFinderMetabo, and peakonly in recall rates and correlation with sample concentrations. Five datasets of different instruments and samples were used to evaluate the quality of PICs and the universal applicability of DeepPIC, and 95.12% of the found PICs could precisely match their manually labeled PICs. Therefore, KPIC2+DeepPIC is an automatic, practical, and off-the-shelf method to extract features from raw data directly, exceeding traditional methods with careful parameter tuning. It is publicly available at
    Keywords:  Deep learning; LC-MS; Pure ion chromatogram
  10. Methods Mol Biol. 2023 ;2688 41-54
      Desorption electrospray ionization (DESI) is an ambient technique that allows chemical information to be obtained directly from a wide range of surfaces, without pretreatment. Here we describe the improvements that have been developed to be able to achieve low tens of microns pixel size MSI experiments with high sensitivity for metabolites and lipids from biological tissue sections.In the last decade, DESI mass spectrometry has undergone developmental improvements, with regard to the method of desorption and ionization as well as the mass spectrometer to which the DESI source has been coupled to. DESI is becoming a mass spectrometry imaging technique, which can match and complement the currently most widely adopted ionization technique, the matrix-assisted laser desorption/ionization (MALDI).
    Keywords:  Ambient; Co-registration; DESI; Heated transfer line; High definition imaging
  11. J Chromatogr A. 2023 Jun 30. pii: S0021-9673(23)00405-3. [Epub ahead of print]1705 464179
      Low-molecular-weight heparins (LMWHs) are important anticoagulants widely used in clinic. Since they are comprised of complex and heterogenous glycan chains, liquid chromatography-tandem mass spectrometry (LC-MS) is commonly used for structural analysis and quality control of LMWHs to ensure their safety and efficacy. Yet, the structural complexity arising from the parent heparin macromolecules, as well as the different depolymerization methods used for preparing LMWHs, makes processing and assigning the LC-MS data of LWMHs very tedious and challenging. We therefore developed, and here report, an open-source and easy-to-use web application, MsPHep, to facilitate the LMWH analysis based on LC-MS data. MsPHep is compatible with various LMWHs and chromatographic separation methods. With the HepQual function, MsPHep is capable of annotating both the LMWH compound and its isotopic distribution from mass spectra. Moreover, the HepQuant function enables automatic quantification of LMWH compositions without prior knowledge or any database generation. To demonstrate the reliability and system stability of MsPHep, we tested various types of LMWHs that were analyzed with different chromatographic methods coupled to MS. The results show that MsPHep has its own advantages compared to another public tool GlycReSoft for LMWH analysis, and it is available online under an open-source license at
    Keywords:  LC-MS; LMWH; Structural analysis; Web application
  12. Methods Mol Biol. 2023 ;2688 107-121
      Mass spectrometry imaging has the potential to reveal important molecular interaction in morphological regions in tissue. However, the simultaneous ionization of the continuously altered and complex chemistry in each pixel can introduce artifacts that result in skewed molecular distributions in the compiled ion images. These artifacts are known as matrix effects. Mass spectrometry imaging using nanospray desorption electrospray ionization (nano-DESI MSI) enables the elimination of matrix effects by doping the nano-DESI solvent with internal standards. Carefully selected internal standards ionize similarly and simultaneously with the extracted analytes from thin tissue sections, and the matrix effects are eliminated through a robust data normalization method. Herein we describe the setup and use of pneumatically assisted (PA) nano-DESI MSI with standards doped in the solvent for elimination of matrix effects in ion images.
    Keywords:  Internal standards; Ionization suppression; Mass spectrometry imaging; Matrix effects; Nanospray desorption electrospray ionization; Tissue sections
  13. bioRxiv. 2023 Jun 02. pii: 2023.05.31.543144. [Epub ahead of print]
      Elucidating the spatial-biochemical organization of the brain across different scales produces invaluable insight into the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive chemical profiling of large brain regions in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping via MEISTER, an integrative experimental and computational mass spectrometry framework. MEISTER integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating 3D molecular distribution, and a data integration method fitting cell-specific mass spectra to 3D data sets. We imaged detailed lipid profiles in tissues with data sets containing millions of pixels, and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents, and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future developments of multiscale technologies for biochemical characterization of the brain.
  14. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Jun 30. pii: S1570-0232(23)00219-2. [Epub ahead of print]1227 123809
      Cypate, a heptamethine cyanine dye, is a prototypic near-infrared (NIR) theranostic agent for optical imaging and photothermal therapy. In the present study, a selective, sensitive, and rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the quantitation of cypate in mouse plasma. The chromatographic separation was achieved using a short C18 column (2.1 mm × 50 mm, 5 μm) with a run time of 5 min. The MS was operated in multiple reaction monitoring (MRM) mode via positive electrospray ionization. The ion transitions for cypate and internal standard IR-820 were m/z 626.3 → 596.3 and m/z 827.4 → 330.2, respectively. The method was linear over a concentration range of 1.0-500 ng/mL. The within-run and between-run precision was less than 14.4% with accuracy in the range of -13.4% ∼ 9.8%. The validated method was successfully applied to a pharmacokinetic study of cypate in mice following intravenous administration.
    Keywords:  Cyanine dye; Cypate; IR-820; LC-MS/MS; Pharmacokinetics
  15. bioRxiv. 2023 Jun 03. pii: 2023.06.02.543480. [Epub ahead of print]
      Compatible with label-free detection and quantification, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of biomolecules in intact specimens. Yet, the spatial resolution of MSI is limited by the method's physical and instrumental constraints, which often preclude it from single-cell and subcellular applications. By taking advantage of the reversible interaction of analytes with superabsorbent hydrogels, we developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome these limits. With GAMSI, the spatial resolution of lipid and protein MALDI-MSI can be enhanced severalfold without changing the existing mass spectrometry hardware and analysis pipeline. This approach will further enhance the accessibility to (sub)cellular-scale MALDI-MSI-based spatial omics.
  16. bioRxiv. 2023 Jun 01. pii: 2023.06.01.543311. [Epub ahead of print]
      Acetyl-Coenzyme A is a central metabolite in catabolic and anabolic pathways as well as the acyl donor for acetylation reactions. Multiple quantitative measurement techniques for acetyl-CoA have been reported, including commercially available kits. Comparisons between techniques for acetyl-CoA measurement have not been reported. This lack of comparability between assays makes context-specific assay selection and interpretation of results reporting changes in acetyl-CoA metabolism difficult. We compared commercially available colorimetric ELISA and fluorometric enzymatic-based kits to liquid chromatography-mass spectrometry-based assays using tandem mass spectrometry (LC-MS/MS) and high-resolution mass spectrometry (LC-HRMS). The colorimetric ELISA kit did not produce interpretable results even with commercially available pure standards. The fluorometric enzymatic kit produced comparable results to the LC-MS-based assays depending on matrix and extraction. LC-MS/MS and LC-HRMS assays produced well-aligned results, especially when incorporating stable isotope-labeled internal standards.
  17. Anal Chem. 2023 Jul 06.
      Polyphenols, prevalent in plants and fungi, are investigated intensively in nutritional and clinical settings because of their beneficial bioactive properties. Due to their complexity, analysis with untargeted approaches is favorable, which typically use high-resolution mass spectrometry (HRMS) rather than low-resolution mass spectrometry (LRMS). Here, the advantages of HRMS were evaluated by thoroughly testing untargeted techniques and available online resources. By applying data-dependent acquisition on real-life urine samples, 27 features were annotated with spectral libraries, 88 with in silico fragmentation, and 113 by MS1 matching with PhytoHub, an online database containing >2000 polyphenols. Moreover, other exogenous and endogenous molecules were screened to measure chemical exposure and potential metabolic effects using the Exposome-Explorer database, further annotating 144 features. Additional polyphenol-related features were explored using various non-targeted analysis techniques including MassQL for glucuronide and sulfate neutral losses, and MetaboAnalyst for statistical analysis. As HRMS typically suffers a sensitivity loss compared to state-of-the-art LRMS used in targeted workflows, the gap between the two instrumental approaches was quantified in three spiked human matrices (urine, serum, plasma) as well as real-life urine samples. Both instruments showed feasible sensitivity, with median limits of detection in the spiked samples being 10-18 ng/mL for HRMS and 4.8-5.8 ng/mL for LRMS. The results demonstrate that, despite its intrinsic limitations, HRMS can readily be used for comprehensively investigating human polyphenol exposure. In the future, this work is expected to allow for linking human health effects with exposure patterns and toxicological mixture effects with other xenobiotics.
  18. J Pharm Biomed Anal. 2023 Jun 10. pii: S0731-7085(23)00274-1. [Epub ahead of print]234 115505
      A high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed for the analysis of itraconazole (ITZ) and hydroxyitraconazole (ITZ-OH) as part of a human pharmacokinetic study of novel tablet formulations. We demonstrated that 100 µL of plasma sample can be used with a protein precipitation extraction by optimizing different composition of acid in organic solvent for the precipitation solvent, giving comparable recovery to more time-consuming liquid-liquid or solid phase extractions. Additionally, we have shown that by monitoring the halogen isotopic peak for ITZ as well as optimizing chromatographic conditions, we are able to avoid carryover and endogenous interferences, allowing for a lower limit of quantification for our study. We validated the method to quantify ITZ and ITZ-OH from 1 to 250 ng/mL in human plasma and applied this to a formulation research clinical study (NCT04035187). This is the first itraconazole study to demonstrate robustness of the assay by performing interference testing of over-the-counter and common co-administered medications. We are also the first publication to perform incurred sample reanalysis (ISR) at the conclusion of a 672 sample clinical study to show reproducibility of assay performance.
    Keywords:  Clinical trial; Incurred Sample Reanalysis (ISR); Itraconazole; Liquid chromatography tandem mass spectrometry (LC-MS/MS); Poorly soluble
  19. Methods Mol Biol. 2023 ;2688 147-159
      Multimodal mass spectrometry imaging (MSI) is a leading approach for investigating the molecular processes within biological samples. The parallel detection of compounds including metabolites, lipids, proteins, and metal isotopes allows for a more holistic understanding of tissue microenvironments. Universal sample preparation is a primary enabler for samples of the same set to be run across multiple modalities. Using the same method and materials for a cohort of samples reduces any potential variability during sample preparation and allows for comparable analysis across analytical imaging techniques. Here, the MSI workflow is describing a sample preparation protocol for the analysis of three-dimensional (3D) cell culture models. The analysis of biologically relevant cultures by multimodal MSI offers a method in which models of cancer and disease can be studied for the use in early-stage drug development.
    Keywords:  3D cell culture; DESI; IMC; LA-ICP; Multimodal MSI
  20. Bioinformatics. 2023 Jul 04. pii: btad397. [Epub ahead of print]
      MOTIVATION: One central goal of systems biology is to infer biochemical regulations from large-scale OMICS data. Many aspects of cellular physiology and organismal phenotypes can be understood as results of metabolic interaction network dynamics. Previously, we have proposed a convenient mathematical method which addresses this problem using metabolomics data for the inverse calculation of biochemical Jacobian matrices revealing regulatory checkpoints of biochemical regulations. The proposed algorithms for this inference are limited by two issues: they rely on structural network information that needs to be assembled manually, and they are numerically unstable due to ill-conditioned regression problems for large-scale metabolic networks.RESULTS: To address these problems we developed a novel regression-loss based inverse Jacobian algorithm, combining metabolomics COVariance and genome-scale metabolic RECONstruction, which allows for a fully automated, algorithmic implementation of the COVRECON workflow. It consists of two parts: a, Sim-Network and b, Inverse differential Jacobian evaluation. Sim-Network automatically generates an organism-specific enzyme and reaction dataset from Bigg and KEGG databases, which is then used to reconstruct the Jacobian's structure for a specific metabolomics dataset. Instead of directly solving a regression problem as in the previous workflow, the new inverse differential Jacobian is based on a substantially more robust approach and rates the biochemical interactions according to their relevance from large-scale metabolomics data.The approach is illustrated by in silico stochastic analysis with differently-sized metabolic networks from the BioModels database and applied to a real-world example. The characteristics of the COVRECON implementation are that i) it automatically reconstructs a data-driven superpathway model; ii) more general network structures can be investigated and iii) the new inverse algorithm improves stability, decreases computation time, and extends to large-scale models.
    AVAILABILITY: The code is available in the website
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  21. J Sep Sci. 2023 Jul 04. e2300207
      Hydroxylated polycyclic aromatic hydrocarbons are metabolites of persistent organic pollutants which are formed during the bioactivation process of biological matrices and whose toxicity is being studied. The aim of this work was the development of a novel analytical method for the determination of these metabolites in human tissues, known to have bioaccumulated their parent compounds. Samples were treated by salting-out assisted liquid-liquid extraction and the extracts were analyzed by ultra-high performance liquid chromatography coupled to mass spectrometry with a hybrid quadrupole-time-of-flight analyzer. The proposed method achieved limits of detection in the 0.15-9.0 ng/g range for the five target analytes (1-hydroxynaphthalene, 1-hydroxypyrene, 2-hydroxynaphthalene, 7-hydroxybenzo[a]pyrene, and 9-hydroxyphenanthrene). The quantification was achieved by matrix-matched calibration using 2,2´-biphenol as internal standard. For all compounds, relative standard deviation, calculated for six successive analyses, was below 12.1%, demonstrating good precision for the developed method. None of the target compounds was detected in the 34 studied samples. Moreover, an untargeted approach was applied to study the presence of other metabolites in the samples, as well as their conjugated forms and related compounds. For this objective, a homemade mass spectrometry database covering 81 compounds was created and none of them was detected in the samples.
    Keywords:  high-resolution mass spectrometry; human tissues; hydroxylated polycyclic aromatic hydrocarbons; liquid chromatography; salting out liquid-liquid extraction
  22. J Sep Sci. 2023 Jul 03. e2300214
      The development of a fast, cost-effective, and efficient microextraction by packed sorbent setup was achieved by combining affordable laboratory-repackable devices of microextraction with a high-throughput cartesian robot. This setup was evaluated for the development of an analytical method to determine N-nitrosamines in losartan tablets. N-nitrosamines pose a significant concern in the pharmaceutical market due to their carcinogenic risk, necessitating their control and quantification in pharmaceutical products. The parameters influencing the performance of this sample preparation for N-nitrosamines were investigated through both univariate and multivariate experiments. Microextractions were performed using just 5.0 mg of carboxylic acid-modified polystyrene divinylbenzene copolymer as the extraction phase. Under the optimized conditions, the automated setup enabled the simultaneous treatment of six samples in less than 20 min, providing reliable analytical confidence for the proposed application. The analytical performance of the automated high-throughput microextraction by the packed sorbent method was evaluated using a matrix-matching calibration. Quantification was performed using ultra-high-performance liquid chromatography-tandem mass spectrometry with chemical ionization at atmospheric pressure. The method exhibited limits of detection as low as 50 ng/g, good linearity, and satisfactory intra-day (1.38-18.76) and inter-day (2.66-20.08) precision. Additionally, the method showed accuracy ranging from 80% to 136% for these impurities in pharmaceutical formulations.
    Keywords:  N-nitrosamines; losartan; microextraction; pharmaceutical impurities; sample automatization
  23. Methods Mol Biol. 2023 ;2688 27-40
      Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has seen a growing interest as a leading technique in the pharmaceutical industry for mapping label-free exogenous and endogenous species in biological tissues. However, the use of MALDI-MSI to perform spatially resolved absolute quantitation of species directly in tissues is still challenging, and robust quantitative mass spectrometry imaging (QMSI) methods need to be developed. In this study, we describe the microspotting technique for analytical and internal standard deposition, matrix sublimation, powerful QMSI software, and mass spectrometry imaging setup to obtain absolute quantitation of drug distribution in 3D skin models.
    Keywords:  3D skin models; Internal standard; MALDI-MSI; Microspotting; QMSI; Quantitation
  24. Chemosphere. 2023 Jun 29. pii: S0045-6535(23)01628-4. [Epub ahead of print] 139361
      Implementing effective environmental management strategies requires a comprehensive understanding of the chemical composition of environmental pollutants, particularly in complex mixtures. Utilizing innovative analytical techniques, such as high-resolution mass spectrometry and predictive retention index models, can provide valuable insights into the molecular structures of environmental contaminants. Liquid Chromatography-High-Resolution Mass Spectrometry is a powerful tool for the identification of isomeric structures in complex samples. However, there are some limitations that can prevent accurate isomeric structure identification, particularly in cases where the isomers have similar mass and fragmentation patterns. Liquid chromatographic retention, determined by the size, shape, and polarity of the analyte and its interactions with the stationary phase, contains valuable 3D structural information that is vastly underutilized. Therefore, a predictive retention index model is developed which is transferrable to LC-HRMS systems and can assist in the structural elucidation of unknowns. The approach is currently restricted to carbon, hydrogen, and oxygen-based molecules <500 g mol-1. The methodology facilitates the acceptance of accurate structural formulas and the exclusion of erroneous hypothetical structural representations by leveraging retention time estimations, thereby providing a permissible tolerance range for a given elemental composition and experimental retention time. This approach serves as a proof of concept for the development of a Quantitative Structure-Retention Relationship model using a generic gradient LC approach. The use of a widely used reversed-phase (U)HPLC column and a relatively large set of training (101) and test compounds (14) demonstrates the feasibility and potential applicability of this approach for predicting the retention behaviour of compounds in complex mixtures. By providing a standard operating procedure, this approach can be easily replicated and applied to various analytical challenges, further supporting its potential for broader implementation.
    Keywords:  HPLC-HRMS; In silico prediction; Quantitative structure- retention relationship model; Retention index; Structural elucidation
  25. Curr Opin Chem Biol. 2023 Jul 04. pii: S1367-5931(23)00100-X. [Epub ahead of print]76 102362
      Mass spectrometry imaging (MSI) is an emerging technology in cancer metabolomics. Desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) MSI are complementary techniques to identify hundreds of metabolites in space with close to single-cell resolution. This technology leap enables research focusing on tumor heterogeneity, cancer cell plasticity, and the communication signals between cancer and stromal cells in the tumor microenvironment (TME). Currently, unprecedented knowledge is generated using spatial metabolomics in fundamental cancer research. Yet, also translational applications are emerging, including the assessment of spatial drug distribution in organs and tumors. Moreover, clinical research investigates the use of spatial metabolomics as a rapid pathology tool during cancer surgeries. Here, we summarize MSI applications, the knowledge gained by this technology in space, future directions, and developments needed.
    Keywords:  Cancer cell plasticity; Cancer research; Labelled isotope tracing; Mass spectrometry imaging; Metabolite identification; Metabolomics; Tumor heterogeneity; Tumor microenvironment (TME)