bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒07‒16
25 papers selected by
Sofia Costa

  1. bioRxiv. 2023 Jun 29. pii: 2023.06.26.546628. [Epub ahead of print]
      Combined multi-omics analysis of proteomics, polar metabolomics, and lipidomics requires separate liquid chromatography-mass spectrometry (LC-MS) platforms for each omics layer. This requirement for different platforms limits throughput and increases costs, preventing the application of mass spectrometry-based multi-omics to large scale drug discovery or clinical cohorts. Here, we present an innovative strategy for simultaneous multi-omics analysis by direct infusion (SMAD) using one single injection without liquid chromatography. SMAD allows quantification of over 9,000 metabolite m/z features and over 1,300 proteins from the same sample in less than five minutes. We validated the efficiency and reliability of this method and then present two practical applications: mouse macrophage M1/M2 polarization and high throughput drug screening in human 293T cells. Finally, we demonstrate relationships between proteomic and metabolomic data are discovered by machine learning.
  2. J Biomol Tech. 2023 07 01. pii: 3fc1f5fe.1972c438. [Epub ahead of print]34(2):
      Multiple reaction monitoring (MRM) profiling is a strategy for the exploratory analysis of small molecules and lipids by direct sample injection, ie, without the use of chromatographic separation. It is based on instrument methods that comprise a list of ion transitions (MRMs), in which the precursor ion is the expected ionized m/z of the lipid at its species level, ie, the description of lipid class and number of carbon and double bonds in the fatty acid chain(s), and the product ion is a fragment expected for the lipid class or for the fatty acid neutral loss. The Lipid Maps database is expanding constantly, and therefore the MRM-profiling methods associated with this database need to be continuously updated. Here, we provide a comprehensive overview and the key references for the MRM-profiling methodology and workflow, followed by a step-by-step approach to build MRM-profiling instrument acquisition methods for class-based lipid exploratory analysis based on the Lipid Maps database. The detailed workflow includes (1) importing the list of lipids from the database; (2) for a given class, combining isomeric lipids described at full structural level into 1 entry to obtain the neutral mass at species level; (3) attributing the standard Lipid Maps abbreviated nomenclature for the lipid at its species level; (4) predicting the ionized precursor ions; and (5) adding the expected product ion. We also describe how to simulate the precursor ion for the suspect screening of modified lipids using lipid oxidation and their expected product ions as an example. After determining the MRMs, information about collision energy, dwell time, and other instrument parameters are added to finalize the acquisition method. As an example of final method output, we describe the format for Agilent MassHunter v.B.06 and provide the parameters in which optimization can be performed by lipid class using one or more lipid standards.
    Keywords:  MRM profiling; direct injection analysis; exploratory analysis; lipids
  3. Nat Commun. 2023 07 11. 14(1): 4113
      Significant challenges remain in the computational processing of data from liquid chomratography-mass spectrometry (LC-MS)-based metabolomic experiments into metabolite features. In this study, we examine the issues of provenance and reproducibility using the current software tools. Inconsistency among the tools examined is attributed to the deficiencies of mass alignment and controls of feature quality. To address these issues, we develop the open-source software tool asari for LC-MS metabolomics data processing. Asari is designed with a set of specific algorithmic framework and data structures, and all steps are explicitly trackable. Asari compares favorably to other tools in feature detection and quantification. It offers substantial improvement in computational performance over current tools, and it is highly scalable.
  4. J Mass Spectrom. 2023 Jul;58(7): e4958
      Quantification of pharmaceutical compounds using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is an alternative to traditional liquid chromatography (LC)-MS techniques. Benefits of MALDI-based approaches include rapid analysis times for liquid samples and imaging mass spectrometry capabilities for tissue samples. As in most quantification experiments, the use of internal standards can compensate for spot-to-spot and shot-to-shot variability associated with MALDI sampling. However, the lack of chromatographic separation in traditional MALDI analyses results in diminished peak capacity due to the chemical noise background, which can be detrimental to the dynamic range and limit of detection of these approaches. These issues can be mitigated by using a hybrid mass spectrometer equipped with a quadrupole mass filter (QMF) that can be used to fractionate ions based on their mass-to-charge ratios. When the masses of the analytes and internal standards are sufficiently disparate in mass, it can be beneficial to effect multiple narrow mass isolation windows using the QMF, as opposed to a single wide mass isolation window, to minimize chemical noise while allowing for internal standard normalization. Herein, we demonstrate a MALDI MS quantification workflow incorporating multiple sequential mass isolation windows enabled on a QMF, which divides the total number of MALDI laser shots into multiple segments (i.e., one segment for each mass isolation window). This approach is illustrated through the quantitative analysis of the pharmaceutical compound enalapril in human plasma samples as well as the simultaneous quantification of three pharmaceutical compounds (enalapril, ramipril, and verapamil). Results show a decrease in the limit of detection, relative standard deviations below 10%, and accuracy above 85% for drug quantification using multiple mass isolation windows. This approach has also been applied to the quantification of enalapril in brain tissue from a rat dosed in vitro. The average concentration of enalapril determined by imaging mass spectrometry is in agreement with the concentration determined by LC-MS, giving an accuracy of 104%.
    Keywords:  imaging mass spectrometry; ion isolation; pharmaceutical; quantification
  5. J Agric Food Chem. 2023 Jul 11.
      Cereals contain lipids that fulfill important physiological roles and are associated with stress in the plant. However, many of the specific biological roles of lipids are yet unknown. Comprehensive analysis of these polar lipid categories in whole grain wheat and oat, cereals highly relevant also in nutrition, was performed. Hydrophilic interaction liquid chromatography (HILIC) and reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with high-resolution mass spectrometry using electrospray ionization in both positive and negative ionization mode was used. Exploiting the different separation mechanisms, HILIC was used as a screening method for straightforward lipid class assignment and enabled differentiation of isomeric lipid classes, like phosphatidylethanolamine and lyso-N-acylphosphatidylethanolamine, while RP-HPLC facilitated separation of constitutional isomers. In combination with data-dependent MS/MS experiments, 67 lipid species belonging to nine polar lipid classes could be identified. Furthermore, with both ionization modes, fatty acyl chains directly connected to the lipid headgroups could be assigned. This work focused on the four lipid classes N-acylphosphatidylethanolamines, acyl-monogalactosyldiacylglycerols, digalactosyldiacylglycerols, and monogalactosyldiacylglycerols as they were less studied in detail in the past. Applying the complementary approach, the relative lipid species compositions in these lipid classes was investigated in detail.
    Keywords:  Hydrophilic Interaction Liquid Chromatography (HILIC); cereals; glycolipids; high-resolution mass spectrometry; lipids; phospholipids; reversed-phase HPLC
  6. J Pharm Biomed Anal. 2023 Jul 05. pii: S0731-7085(23)00325-4. [Epub ahead of print]234 115556
      A rapid preparation method for the analysis of the urine from a cannabis user was established. Generally, 11-nor-9-carboxy-∆9-tetrahydrocannabinol (THC-COOH), which is one of the main metabolites of ∆9-tetrahydorocannabinol (THC), must be detected from a user's urine to verify cannabis use. However, existing preparation methods are usually multistep and time-consuming processes. Before the analysis by liquid-chromatography tandem mass spectrometry (LC-MS/MS), deconjugation by treatment with β-glucuronidase or alkaline solution, liquid-liquid extraction or solid-phase extraction (SPE), and evaporation are generally performed. In addition, subsequent derivatization (silylation or methylation) are certainly necessary for gas-chromatography mass spectrometry (GC/MS) analysis. Here, we focused on the phenylboronic-acid (PBA) SPE, which selectively binds compounds with a cis-diol moiety. THC-COOH is metabolized as a glucuronide conjugate (THC-COOGlu) which has cis-diol moieties, therefore, we investigated the conditions of its retention and elution to reduce the operating time. We developed four elution conditions, which afford the following derivatives: acidic elution for THC-COOGlu, alkaline elution for THC-COOH, methanolysis elution for the THC-COOH methyl ester (THC-COOMe), and methanolysis elution and following methyl etherification for O-methyl-THC-COOMe (O-Me-THC-COOMe). All repeatability and recovery rates were evaluated by LC-MS/MS in this study. As a result, these four pathways required short times (within 10-25 min) and exhibited good repeatability and recovery rates. Detection limits of pathway I-IV were 10.8, 1.7, 18.9, and 13.8 ng mL-1, respectively. Lower limits of quantification were 62.5, 31.25, 57.3, and 62.5 ng mL-1, respectively. When proof of cannabis use is required, any elution condition can be selected to match the possessing reference standards and analytical instruments. To our knowledge, this is the first report of using PBA SPE for the preparation of the urine samples containing cannabis and achieving partial derivatization when eluting from a PBA carrier. Our method can provide a new and practical solution for the preparation of the urine samples from cannabis users. Although the PBA SPE method cannot recover THC-COOH in urine because of its lack of a 1,2-diol moiety, this method has technological advantages for simplifying the process and reducing the operating time, thereby avoiding human errors.
    Keywords:  11-nor-9-carboxy-∆(9)-tetrahydrocannabinol; Glucuronide; LC-MS/MS; Phenylboronic acid; Preparation; Solid-phase extraction (SPE)
  7. Adv Exp Med Biol. 2023 ;1415 37-42
      The molecular characterization of extracellular deposits is crucial to understanding the clinical progression of AMD. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis is a powerful analytical discovery tool capable of identifying lipids in an untargeted manner. NanoLC-MS/MS is an analytical tool capable of identifying lipids with high sensitivity and minimum sample usage. Hence, the purpose of this study was to compare retina lipid identification from RPE-choroid samples using high flow LC-MS/MS and nanoLC-MS/MS. Manually dissected paraformaldehyde-fixed human donor tissues sections were used for LC-MS/MS and nanoLC-MS/MS analysis. Lipids were extracted with MeOH/MTBE/CHCl3 (MMC) and were analyzed by LC-MS/MS and nanoLC-MS/MS using negative and positive ionization modes. Untargeted lipidomics using LC-MS/MS identified 215 lipids from 4 lipid classes and 15 subclasses. We observed a 78% increase in lipid identifications using nanoLC-MS/MS with lipid numbers totaling 384. The nanoLC-MS/MS method is expected to provide extensive lipid identifications from small retina samples, e.g., from drusen and drusenoid deposits in aged and AMD eyes, and could help elucidate how lipids are involved in extracellular deposit formation in AMD.
    Keywords:  Age-related macular degeneration; Fixed; LC-MS/MS; Lipids; NanoLC-MS/MS; RPE; Retina
  8. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Jul 04. pii: S1570-0232(23)00223-4. [Epub ahead of print]1227 123813
      The proposed research was focused on the development of a gas chromatography-tandem mass spectrometry (GC-QqQ-MS) method under milder electron ionization (EI) conditions for the assay of vitamin D metabolites in human serum. Efficiency of three different silylation agents was evaluated for the conversion of vitamin D species into trimethylsilyl (TMS) derivatives, among which N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) proved to be the most effective. Indeed, the MSTFA reagent was able to convert in TMS ether even the 25-hydroxyl vitamin D derivative that, as known, possesses steric hindrance problems. The separation of vitamin D compounds was obtained in about 11.5 min using a narrow-bore column of dimensions 30 m × 0.25 mm ID × 0.10 μm df with a poly(5% diphenyl/95% dimethyl siloxane) stationary phase. The mass spectrometry ionization of the silylated derivatives was performed under milder EI conditions (20-eV energy) that, respect to common 70-eV energy, generated scan mass spectra with higher relative and absolute intensities of high-mass diagnostic ions, along with a reduced abundance of the low-mass. The signals of the ionized compounds were acquired in multi-reaction-monitoring (MRM) mode, thus enabling the obtainment of highly-sensitive and selective quantitative data. The developed method was validated in term of linearity, accuracy, limits of detection (LoD) and quantification (LoQ). In detail, regression coefficients of the calibration curves were between 0.9959 and 0.9999; LoDs ranged from 0.06 ng mL-1 to 0.73 ng mL-1 and LoQs from 0.16 ng mL-1 to 2.45 ng mL-1. With respect to accuracy, the serum SRM 972a certified reference material (Vitamin D metabolites in frozen human serum) (Levels 1-4) was analyzed.
    Keywords:  Cholecalciferol; Ergocalciferol; Gas chromatography; NIST SRM 972a; Soft ionization; Tandem mass spectrometry; Vitamin D
  9. Anal Bioanal Chem. 2023 Jul 11.
      Targeted biomonitoring studies quantifying the concentration of zeranols in biological matrices have focused on liquid chromatography interfaced to mass spectrometry (LC-MS). The MS platform for measurement, quadrupole, time-of-flight (ToF), ion trap, etc., is often chosen based on either sensitivity or selectivity. An instrument performance comparison of the benefits and limitations using matrix-matched standards containing 6 zeranols on 4 MS instruments, 2 low-resolution (linear ion traps), and 2 high-resolution (Orbitrap and ToF) was undertaken to identify the best measurement platform for multiple biomonitoring projects characterizing the endocrine disruptive properties of zeranols. Analytical figures of merit were calculated for each analyte to compare instrument performance across platforms. The calibration curves had correlation coefficients r = 0.989 ± 0.012 for all analytes and LODs and LOQs were ranked for sensitivity: Orbitrap > LTQ > LTQXL > G1 (V mode) > G1 (W mode). The Orbitrap had the smallest measured variation (lowest %CV), while the G1 had the highest. Instrumental selectivity was calculated using full width at half maximum (FWHM) and as expected, the low-resolution instruments had the broadest spectrometric peaks, concealing coeluting peaks under the same mass window as the analyte. Multiple peaks from concomitant ions, unresolved at low resolution (within a unit mass window), were present but did not match the exact mass predicted for the analyte. For example, the high-resolution platforms were able to differentiate between a concomitant peak at 319.1915 from the analyte at 319.1551, included in low-resolution quantitative analyses demonstrating the need to consider coeluting interfering ions in biomonitoring studies. Finally, a validated method using the Orbitrap was applied to human urine samples from a pilot cohort study.
    Keywords:  HRMS; Linear ion trap MS; Low-resolution MS; Orbitrap; Synapt G1; Zearalenone
  10. Molecules. 2023 Jun 21. pii: 4905. [Epub ahead of print]28(13):
      Reliable quantification in biological systems of endogenous low- and high-molecular substances, drugs and their metabolites, is of particular importance in diagnosis and therapy, and in basic and clinical research. The analytical characteristics of analytical approaches have many differences, including in core features such as accuracy, precision, specificity, and limits of detection (LOD) and quantitation (LOQ). Several different mathematic approaches were developed and used for the comparison of two analytical methods applied to the same chemical compound in the same biological sample. Generally, comparisons of results obtained by two analytical methods yields different quantitative results. Yet, which mathematical approach gives the most reliable results? Which mathematical approach is best suited to demonstrate agreement between the methods, or the superiority of an analytical method A over analytical method B? The simplest and most frequently used method of comparison is the linear regression analysis of data observed by method A (y) and the data observed by method B (x): y = α + βx. In 1986, Bland and Altman indicated that linear regression analysis, notably the use of the correlation coefficient, is inappropriate for method-comparison. Instead, Bland and Altman have suggested an alternative approach, which is generally known as the Bland-Altman approach. Originally, this method of comparison was applied in medicine, for instance, to measure blood pressure by two devices. The Bland-Altman approach was rapidly adapted in analytical chemistry and in clinical chemistry. To date, the approach suggested by Bland-Altman approach is one of the most widely used mathematical approaches for method-comparison. With about 37,000 citations, the original paper published in the journal The Lancet in 1986 is among the most frequently cited scientific papers in this area to date. Nevertheless, the Bland-Altman approach has not been really set on a quantitative basis. No criteria have been proposed thus far, in which the Bland-Altman approach can form the basis on which analytical agreement or the better analytical method can be demonstrated. In this article, the Bland-Altman approach is re-valuated from a quantitative bioanalytical perspective, and an attempt is made to propose acceptance criteria. For this purpose, different analytical methods were compared with Gold Standard analytical methods based on mass spectrometry (MS) and tandem mass spectrometry (MS/MS), i.e., GC-MS, GC-MS/MS, LC-MS and LC-MS/MS. Other chromatographic and non-chromatographic methods were also considered. The results for several different endogenous substances, including nitrate, anandamide, homoarginine, creatinine and malondialdehyde in human plasma, serum and urine are discussed. In addition to the Bland-Altman approach, linear regression analysis and the Oldham-Eksborg method-comparison approaches were used and compared. Special emphasis was given to the relation of difference and mean in the Bland-Altman approach. Currently available guidelines for method validation were also considered. Acceptance criteria for method agreement were proposed, including the slope and correlation coefficient in linear regression, and the coefficient of variation for the percentage difference in the Bland-Altman and Oldham-Eksborg approaches.
    Keywords:  Bland and Altman approach; Eksborg; Oldham; agreement; biomarkers; comparison; linear regression analysis; mass spectrometry; tandem mass spectrometry; validation
  11. J Am Soc Mass Spectrom. 2023 Jul 09.
      MALDI-TOF MS is a powerful tool to analyze biomolecules, owing to its soft ionization nature that generally results in simple spectra of singly charged ions. Implementation of the technology in the imaging mode provides a means to spatially map analytes in situ. Recently, a new matrix, DBDA (N1,N4-dibenzylidenebenzene-1,4-diamine) was reported to facilitate the ionization of free fatty acids in negative ion mode. Building on this finding, we sought to implement DBDA for MALDI mass spectrometry imaging studies in brain tissue and successfully map oleic acid, palmitic acid, stearic acid, docosahexaenoic acid, and arachidonic acid using mouse brain sections. Moreover, we hypothesized that DBDA would provide superior ionization for sulfatides, a class of sulfolipids with multiple biological functions. Herein, we also demonstrate that DBDA is ideal for MALDI mass spectrometry imaging of fatty acids and sulfatides in brain tissue sections. Additionally, we show enhanced ionization of sulfatides using DBDA compared with three different traditionally used MALDI matrices. Together these results provide new opportunities for studies to measure sulfatides by MALDI-TOF MS.
  12. Anal Chem. 2023 Jul 10.
      Herein, we assess the complementarity and complexity of data that can be detected within mammalian lipidome mass spectrometry imaging (MSI) via matrix-assisted laser desorption ionization (MALDI) and nanospray desorption electrospray ionization (nano-DESI). We do so by employing 21 T Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with absorption mode FT processing in both cases, allowing unmatched mass resolving power per unit time (≥613k at m/z 760, 1.536 s transients). While our results demonstrated that molecular coverage and dynamic range capabilities were greater in MALDI analysis, nano-DESI provided superior mass error, and all annotations for both modes had sub-ppm error. Taken together, these experiments highlight the coverage of 1676 lipids and serve as a functional guide for expected lipidome complexity within nano-DESI-MSI and MALDI-MSI. To further assess the lipidome complexity, mass splits (i.e., the difference in mass between neighboring peaks) within single pixels were collated across all pixels from each respective MSI experiment. The spatial localization of these mass splits was powerful in informing whether the observed mass splits were biological or artificial (e.g., matrix related). Mass splits down to 2.4 mDa were observed (i.e., sodium adduct ambiguity) in each experiment, and both modalities highlighted comparable degrees of lipidome complexity. Further, we highlight the persistence of certain mass splits (e.g., 8.9 mDa; double bond ambiguity) independent of ionization biases. We also evaluate the need for ultrahigh mass resolving power for mass splits ≤4.6 mDa (potassium adduct ambiguity) at m/z > 1000, which may only be resolved by advanced FTICR-MS instrumentation.
  13. Molecules. 2023 Jun 25. pii: 4978. [Epub ahead of print]28(13):
      Contraceptive tablets typically contain a combination of two synthetic versions of an estrogen and a progestogen, which work together to inhibit the ovulation process. An accurate and precise quantification of these components is essential for contraceptive producers. In this study, we have developed the first gas chromatography-mass spectrometry (GC-MS) method for the simultaneous quantification of 17α-ethinyl estradiol (EE) and drospirenone (DP) in contraceptive formulations. Under the final working conditions, analytes were extracted from the solid by ultrasound-assisted extraction (15 min) in methanol. The resulting suspension was diluted in ethyl acetate, subjected to centrifugation and, finally, the supernatant was directly injected into the GC-MS system. No derivatization reagents were utilized. To correct for instrumental variations, calibration was performed using the internal standard method, with cholesterol as the internal standard. A good linearity was achieved throughout the calibration range for both EE (3-12 µg mL-1) and DP (300-1200 µg mL-1), with R2 values exceeding 0.99. Trueness, assessed in terms of percentages of recovery, was also found to be satisfactory for both analytes, with recovery rates of 106 ± 8% for EE and 93 ± 9% for DP. Furthermore, intra-day and inter-day precision studies yielded relative standard deviation values below 6% for both analytes. In terms of sensitivity, the instrumental limits of detection were 0.25 µg mL-1 for EE and 6.6 µg mL-1 for DP, and the instrumental limits of quantification 0.82 µg mL-1 for EE and 22 µg mL-1 for DP. The method was successfully applied to the analysis of contraceptive tablets from three different pharmaceutical companies. No differences were observed between the measured and the declared amount of active principle per tablet, demonstrating the applicability of the procedure. In addition, a stability study conducted on both the standards and sample extracts demonstrated that they can be stored at room temperature for a minimum period of seven days.
    Keywords:  contraceptive tablets; drospirenone; ethinyl estradiol; gas chromatography; mass spectrometry
  14. Rapid Commun Mass Spectrom. 2023 Aug 30. 37(16): e9595
      RATIONALE: Toluene is a volatile organic compound used in domestic and industrial applications. The main routes of workplace exposure to toluene are inhalation and dermal contact. As toluene exposure can cause severe nervous system damage, its quantification is crucial to prevent occupational illness. Toluene is metabolized mainly as hippuric acid, S-benzylmercapturic acid and epoxides. These are rapidly converted to o-/p-cresol, which is then excreted in the urine as conjugated glucuronides and sulfates. o-Cresol and its conjugates can be chemically hydrolyzed to form free o-cresol, which can then serve as a urinary biomarker of toluene exposure. Current analytical methods for quantifying o-cresol in hydrolyzed urine are, however, either weakened by interference, are not sensitive enough or require water-sensitive sample preparation. Development of a liquid chromatography-tandem mass spectrometry method for assessing exposure to toluene is thus required.METHOD: Urine samples were acidified and heated to form free o-cresol and then derivatized with dansyl chloride and diluted. Extracts were separated by reverse-phase chromatography on a BEH phenyl column and then analyzed using a triple quadrupole instrument in selected reaction monitoring mode.
    RESULTS: The dansyl chloride derivatization step was optimized to produce the derivative within a reaction time of 3 min. Hydrolysis efficiency in forming free o-cresol from conjugated metabolites was evaluated using o-cresol-β-d-glucuronidespiked human urine: complete hydrolysis occurred in 45 min. Dynamic range was 0.4 to 40 μM, and the method was useful for toluene monitoring in non-occupational (0.1 μmol/mmol creatinine) as well as occupational (0.3 μmol/mmol creatinine) exposure. The calculated limit of detection and limit of quantitation of the method were 0.06 and 0.21 μM, respectively. Intraday and interday precisions were 3.2% and 4.4%, respectively. Method accuracy was established as 99% using ClinChek® urine controls.
    CONCLUSION: An ultrahigh-performance liquid chromatography-tandem mass spectrometry method for analysis of o-cresol was developed for biological monitoring of toluene exposure in human urine. This is the method of choice used by occupational health and safety practitioners in the province of Québec, Canada.
  15. Clin Chem Lab Med. 2023 Jul 13.
      OBJECTIVES: To update traditional "wet" matrices to dried blood spot (DBS) sampling, based on the liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) technique, and develop a method for simultaneous analyzing caffeine and its three primary metabolites (theobromine, paraxanthine, and theophylline), supporting routine therapeutic drug monitoring (TDM) for preterm infants.METHODS: DBS samples were prepared by a two-step quantitative sampling method, i.e., volumetric sampling of a quantitative 10 μL volume of peripheral blood and an 8 mm diameter whole punch extraction by a methanol/water (80/20, v/v) mixture containing 125 mM formic acid. Four paired stable isotope labeled internal standards and a collision energy defect strategy were applied for the method optimization. The method was fully validated following international guidelines and industrial recommendations on DBS analysis. Cross validation with previously developed plasma method was also proceeded. The validated method was then implemented on the TDM for preterm infants.
    RESULTS: The two-step quantitative sampling strategy and a high recovery extraction method were developed and optimized. The method validation results were all within the acceptable criteria. Satisfactory parallelism, concordance, and correlation were observed between DBS and plasma concentrations of the four analytes. The method was applied to provide routine TDM services to 20 preterm infants.
    CONCLUSIONS: A versatile LC-MS/MS platform for simultaneous monitoring caffeine and its three primary metabolites was developed, fully validated, and successfully applied into the routine clinical TDM practices. Sampling method switching from "wet" matrices to "dry" DBS will facilitate and support the precision dosing of caffeine for preterm infants.
    Keywords:  LC-MS/MS; caffeine; dried blood spot; preterm infants; therapeutic drug monitoring
  16. Rapid Commun Mass Spectrom. 2023 Aug 30. 37(16): e9590
      RATIONALE: Ambient ionization mass spectrometry (AIMS) delivers realistic data from samples in their native state. In addition, AIMS methods reduce time and costs for sample preparation and have less environmental impact. However, AIMS data are often complex and require substantial processing before interpretation.METHODS: We developed an interactive R script for guided mass spectrometry (MS) data processing. The "MQ_Assistant" is based on MALDIquant, a popular R package for MS data processing. In each step, the user can try and preview the effect of chosen parameters before deciding on the values with the best result and proceeding to the next stage. The outcome of the MQ_Assistant is a feature matrix that can be further analyzed in R and statistics tools such as MetaboAnalyst.
    RESULTS: Using 360 AIMS example spectra, we demonstrate the step-by-step processing for creating a feature matrix. In addition, we show how to visualize the results of three biological replicates of a plant-microbe interaction between Arabidopsis and Trichoderma as a heatmap using R and upload them to MetaboAnalyst. The final parameter set can be saved for reuse in MALDIquant workflows of similar data.
    CONCLUSIONS: The MQ_Assistant helps novices and experienced users to develop workflows for (AI)MS data processing. The interactive procedure supports the quick finding of appropriate settings. These parameters can be exported and reused in future projects. The stepwise operation with visual feedback also suggests the use of the MQ_Assistant in education.
  17. Biotechnol Bioeng. 2023 Jul 10.
      Human macrophages are innate immune cells with diverse, functionally distinct phenotypes, namely, pro-inflammatory M1 and anti-inflammatory M2 macrophages. Both are involved in multiple physiological and pathological processes, including would healing, infection, and cancer. However, the metabolic differences between these phenotypes are largely unexplored at single-cell resolution. To address this knowledge gap, an untargeted live single-cell mass spectrometry-based metabolomic profiling coupled with a machine-learning data analysis approach was developed to investigate the metabolic profile of each phenotype at the single-cell level. Results show that M1 and M2 macrophages have distinct metabolic profiles, with differential levels of fatty acyls, glycerophospholipids, and sterol lipids, which are important components of plasma membrane and involved in multiple biological processes. Furthermore, we could discern several putatively annotated molecules that contribute to inflammatory response of macrophages. The combination of random forest and live single-cell metabolomics provided an in-depth profile of the metabolome of primary human M1 and M2 macrophages at the single-cell level for the first time, which will pave the way for future studies targeting the differentiation of other immune cells.
    Keywords:  human macrophages; phenotype classification; random forest; single-cell metabolomics
  18. Rapid Commun Mass Spectrom. 2023 Aug 30. 37(16): e9594
      RATIONALE: Sublimation is a solvent-free technique used to apply a uniform matrix coating over a large sample plate, improving the matrix's purity and enhancing the analyte signal. Although the 5-chloro-2-mercaptobenzothiazole (CMBT) matrix was introduced years ago, there are no reports of its application via sublimation. We investigated the experimental parameters that are optimal for CMBT matrix sublimation on mouse kidney samples. We also evaluated the stability of the sublimed CMBT matrix under a vacuum environment. Using kidney samples prepared with a sublimated CMBT matrix, we conducted matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) analysis of specific phospholipids (phosphatidylcholine and phosphatidylglycerol in the positive ion mode and phosphatidylinositol in the negative ion mode). We also explored various spatial resolutions (50, 20, and 10 μm) and performed sequential MALDI-hematoxylin and eosin (H&E) staining.METHODS: The CMBT matrix was applied to kidney samples using a sublimation apparatus connected to a vacuum pump to achieve a pressure of 0.05 Torr. The matrix was then subjected to different temperatures and sublimation times to determine the optimal conditions for matrix application. Subsequently, a Q-Exactive mass spectrometer equipped with a Spectroglyph MALDI ion source was employed for MALDI-MSI experiments. Standard protocols were followed for H&E staining after MALDI analysis.
    RESULTS: A matrix thickness of 0.15 mg/cm2 yielded high-quality images. The sublimated matrix exhibited minimal loss after approximately 20 h of exposure to a vacuum of 7 Torr, indicating its stability under these conditions. Ion images were successfully obtained at spatial resolutions of 50, 20, and 10 μm. Furthermore, orthogonal histological information was obtained through sequential MALDI-H&E staining.
    CONCLUSIONS: We demonstrate that samples prepared for MALDI-MSI using sublimation to apply the CMBT matrix yield high-quality mass spectrometric images of mouse kidney sections. We also provide data for the impact of various experimental parameters on image quality (e.g., temperature, time, matrix thickness, and spatial resolution).
  19. MethodsX. 2023 ;10 102199
      The Regions of Interest Multivariate curve Resolution (ROIMCR) methodology has gained significance for analyzing mass spectrometry data. The new SigSel package improves the ROIMCR methodology by providing a filtering step to reduce computational costs and to identify chemical compounds giving low-intensity signals. SigSel allows the visualization and assessment of ROIMCR results and filters out components resolved as interferences and background noise. This improves the analysis of complex mixtures and facilitates the identification of chemical compounds for statistical or chemometrics analysis. SigSel has been tested using metabolomics samples of mussels exposed to the sulfamethoxazole antibiotic. It begins by analyzing the data according to their charge state, eliminating signals considered background noise, and reducing the size of the datasets. In the ROIMCR analysis, the resolution of 30 ROIMCR components was achieved. After evaluating these components, 24 were ultimately selected explaining 99.05% of the total data variance. From ROIMCR results, chemical annotation is performed using different methods: •Generating a list of signals and reanalyzing them in a data-dependent analysis.•Comparing the ROIMCR resolved mass spectra to those stored in online repositories.•Searching MS signals of chemical compounds in the ROIMCR resolved spectra profiles.
    Keywords:  Chemical compound identification; Mass spectrometry; Metabolomics; Non-target analysis; Quantitative analysis; SigSel
  20. Data Brief. 2023 Aug;49 109313
      CNS injuries of the anuran amphibian, Xenopus laevis, are uniquely suited for studying the molecular compositions of neuronal regeneration of retinal ganglion cells (RGC) due to a functional recovery of optic axons disparate to adult mammalian analogues. RGCs and their optic nerve axons undergo irreversible neurodegeneration in glaucoma and associated optic neuropathies, resulting in blindness in mammals. Conversely, Xenopus demonstrates RGC lifetime-spanning regenerative capabilities after optic nerve crush [1], inciting opportunities to compare de novo regeneration and develop efficient pharmaceutical approaches for vision restoration. Studies revealing lipidome alterations during optic nerve regeneration are sparse and could serve as a solid foundation for these underlying molecular changes. We profile the lipid changes in a transgenic line of 1 year old Xenopus laevis Tg(islet2b:gfp) frogs that were either left untreated (naïve) or had a monocular surgery of either a left optic crush injury (crush) or sham surgery (sham). Matching controls of uninjured right optic nerves were also collected (control). Tg(islet2b:gfp) frogs were allowed to recover for 7,12,18, and 27 days post optic nerve crush. Following euthanasia, the optic nerves were collected for lipidomic analysis. A modified Bligh and Dyer method [2] was used for lipid extraction, followed by untargeted mass spectrometry lipid profiling with a Q Exactive Orbitrap Mass Spectrometer coupled with a Vanquish Horizon Binary UHPLC LC-MS system (LC MS-MS). The raw scans were analyzed and quantified with LipidSearch 5.0 and the statistical analysis was conducted through Metaboanalyst 5.0. This data is available at Metabolomics Workbench, study ID [ST002414].
    Keywords:  Frog; Lipidomics; Optic nerve crush injury; Regeneration
  21. Food Chem. 2023 Jul 05. pii: S0308-8146(23)01330-4. [Epub ahead of print]428 136712
      Excessive use of veterinary drugs in livestock growth poses a threat to food safety. It is, however, challenging to quantify these multi-class veterinary drugs within animal muscles, because of their varied physicochemical properties. In this work, we presented a simple, efficient and sensitive method for the simultaneous determination of multi-class veterinary drugs with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The method involves a highly efficient extraction using a EDTA (pH 7)-ACN (30:70, v/v) solvent system, followed by a one-step solid-phase extraction cleanup approach with PRiME HLB sorbent (Reversed-phase N-vinylpyrrolidone and divinylbenzene copolymer). For all the analytes, over a wide range of polarity, satisfactory recoveries were obtained between 70% and 120%, with relative standard deviations <15%. Excellent sensitivities were achieved with the limits of quantification ranging from 0.2 μg/kg to 3.0 μg/kg. This developed method provides a new targeted strategy for the analysis of multi-class veterinary drugs in muscle matrices.
    Keywords:  Multi-residue analysis; One-step solid-phase extraction; Ultra-high performance liquid chromatography-tandem mass spectrometry; Veterinary drugs
  22. Int J Mol Sci. 2023 Jul 06. pii: 11155. [Epub ahead of print]24(13):
      The tandem mass spectrometry (MS/MS) approach employing an ion trap mass analyzer (IT) was evaluated in isomers recognition. The proposed approach consists of sole, simple, and rapid liquid chromatographic separation (HPLC) without requiring resolution between the analytes. Then, the MS/MS properties were optimized to solve the signal assignment using post-processing data elaboration (LEDA). The IT-MS/MS experiment uses the same site, helium as collision gas, and different time steps to modify the applied conditions on the studied ions. Nevertheless, helium cannot ensure the quick energization of the precursor ion due to its small cross-section. Then, different combinations between excitation amplitude (ExA) and excitation time (ExT) were tested to achieve the activation of the fragmentation channels and the formation of the MS/MS spectrum. Usually, the IT-MS/MS acquisition cycle is longer for other multistage instruments, decreasing the frequency of sample data collection and influencing the chromatographic profile. To solve these problems, two time segments were set up, and the elution conditions were optimized with a compromise between peaks distinction and run time reduction. The developed HPLC-MS/MS method was checked and applied to analyze a series of human plasma samples spiked with an equimolar mixture of pair of isomers.
    Keywords:  ERMS; breakdown curves; collision energy; enzymatic degradation kinetics; ion trap
  23. J Proteome Res. 2023 Jul 10.
      The field of metabolomics has witnessed the development of hundreds of computational tools, but only a few have become cornerstones of this field. While MetaboLights and Metabolomics Workbench are two well-established data repositories for metabolomics data sets, Workflows4Metabolomics and MetaboAnalyst are two well-established web-based data analysis platforms for metabolomics. Yet, the raw data stored in the aforementioned repositories lack standardization in terms of the file system format used to store the associated acquisition files. Consequently, it is not straightforward to reuse available data sets as input data in the above-mentioned data analysis resources, especially for non-expert users. This paper presents CloMet, a novel open-source modular software platform that contributes to standardization, reusability, and reproducibility in the metabolomics field. CloMet, which is available through a Docker file, converts raw and NMR-based metabolomics data from MetaboLights and Metabolomics Workbench to a file format that can be used directly either in MetaboAnalyst or in Workflows4Metabolomics. We validated both CloMet and the output data using data sets from these repositories. Overall, CloMet fills the gap between well-established data repositories and web-based statistical platforms and contributes to the consolidation of a data-driven perspective of the metabolomics field by leveraging and connecting existing data and resources.
    Keywords:  NMR; data analysis; data mining; data sharing; databases; metabolomics
  24. Anal Chem. 2023 Jul 10.
      As the first step of metabolomic analysis in biomarker identification studies, various types of blood collection tubes are used in clinical practice. However, little attention is paid to potential contamination caused by the blank tube itself. Here, we evaluated small molecules in blank EDTA plasma tubes through LC-MS-based untargeted metabolomic analysis and identified small molecules with markedly varied levels among different production batches or specifications. Our data demonstrate possible contamination and data interference caused by blank EDTA plasma tubes when employing large clinical cohorts for biomarker identification. Therefore, we propose a workflow of filtering metabolites in blank tubes prior to statistical analysis to improve the fidelity of biomarker identification.
  25. J Chromatogr A. 2023 Jun 28. pii: S0021-9673(23)00408-9. [Epub ahead of print]1705 464182
      Many contemporary challenges in liquid chromatography-such as the need for "smarter" method development tools, and deeper understanding of chromatographic phenomena-could be addressed more efficiently and effectively with larger volumes of experimental retention data than are available. The paucity of publicly accessible, high-quality measurements needed for the development of retention models and simulation tools has largely been due to the high cost in time and resources associated with traditional retention measurement approaches. Recently we described an approach to improve the throughput of such measurements by using very short columns (typically 5 mm), while maintaining measurement accuracy. In this paper we present a perspective on the characteristics of a dataset containing about 13,000 retention measurements obtained using this approach, and describe a different sample introduction method that is better suited to this application than the approach we used in prior work. The dataset comprises results for 35 different small molecules, nine different stationary phases, and several mobile phase compositions for each analyte/phase combination. During the acquisition of these data, we have interspersed repeated measurements of a small number of compounds for quality control purposes. The data from these measurements not only enable detection of outliers but also assessment of the repeatability and reproducibility of retention measurements over time. For retention factors greater than 1, the mean relative standard deviation (RSD) of replicate (typically n=5) measurements is 0.4%, and the standard deviation of RSDs is 0.4%. Most differences between selectivity values measured six months apart for 15 non-ionogenic compounds were in the range of +/- 1%, indicating good reproducibility. A critically important observation from these analyses is that selectivity defined as retention of a given analyte relative to the retention of a reference compound (kx/kref) is a much more consistent measure of retention over a time span of months compared to the retention factor alone. While this work and dataset also highlight the importance of stationary phase stability over time for achieving reliable retention measurements, we are nevertheless optimistic that this approach will enable the compilation of large databases (>> 10,000 measurements) of retention values over long time periods (years), which can in turn be leveraged to address some of the most important contemporary challenges in liquid chromatography. All the data discussed in the manuscript are provided as Supplemental Information.
    Keywords:  Database; High throughput; Liquid chromatography; Retention; Selectivity