bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒07‒23
28 papers selected by
Sofia Costa

  1. Anal Chim Acta. 2023 Sep 15. pii: S0003-2670(23)00791-2. [Epub ahead of print]1274 341570
      Dipeptides (DPs) have attracted more and more attention in many research fields due to their important biological functions and promising roles as disease biomarkers. However, the determination of DPs in biological samples is very challenging owing to the limited availability of commercial standards, high structure diversity, distinct physical and chemical characteristics, wide concentration range, and the extensive existence of isomers. In this study, a pseudotargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method coupled with chemical derivatization for the simultaneous analysis of 400 DPs and their constructing amino acids (AAs) in biospecimens is established. Dansyl chloride (Dns-Cl) chemical derivatization was introduced to provide characteristic MS fragments for annotation and improve the chromatographic separation of DP isomers. A retention time (RT) prediction model was constructed using 83 standards (63 DPs and 20 AAs) based on their quantitative structural retention relationship (QSRR) after the Dns-Cl labeling, which largely facilitated the annotation of the DPs without standards. Finally, we applied this method to investigate the profile change of DPs in a cisplatin-induced acute kidney injury (AKI) rat model. The established workflow provides a platform to profile DPs and expand our understanding of these little-studied metabolites.
    Keywords:  Acute kidney injury; Cisplatin; Dipeptide; LC-MS/MS; Pseudotargeted metabolomics; Quantitative structural retention relationship
  2. Clin Chem Lab Med. 2023 Jul 19.
      OBJECTIVES: Topiramate is an antiepileptic drug (AED) used for the monotherapy or adjunctive treatment of epilepsy and for the prophylaxis of migraine. It has several pharmacodynamic properties that contribute to both its clinically useful properties and observed adverse effects. Accurate measurement of its concentration is therefore essential for dose adjustment/optimisation of AED therapy. Our aim was to develop and validate a novel reference measurement procedure (RMP) for the quantification of topiramate in human serum and plasma.METHODS: An isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) method in combination with a protein-precipitation-based sample preparation allows for quantification of topiramate in human serum and plasma. To assure traceability to SI units, quantitative nuclear magnetic resonance (qNMR) was applied to characterize the reference material used as primary calibrator for this RMP. Matrix effects were determined by performing a post-column infusion experiment and comparing standard line slopes. Accuracy and precision was evaluated performing an extensive five day precision experiment and measurement uncertainty was evaluated according Guide to the Expression of Uncertainty in Measurement (GUM).
    RESULTS: The method enabled topiramate quantification within the range of 1.20-36.0 μg/mL without interference from structurally related compounds and no evidence of a matrix effect. Intermediate precision was ≤3.2 % and repeatability was 1.4-2.5 % across all concentration levels. The relative mean bias was -0.3 to 3.5 %. Expanded measurement uncertainties for target value assignment (n=6) were found to be ≤2.9 % (k=2) independent of the concentration level and the nature of the sample.
    CONCLUSIONS: In human serum and plasma, the RMP demonstrated high analytical performance for topiramate quantification and fulfilled the requirements on measurement uncertainty. Traceability to SI units was established by qNMR content determination of the topiramate, which was used for direct calibration of the RMP. This RMP is, therefore, fit for purpose for routine assay standardization and clinical sample evaluation.
    Keywords:  SI units; isotope dilution-liquid chromatography-tandem mass spectrometry; qNMR; reference measurement procedure; topiramate; traceability
  3. J Cheminform. 2023 Jul 20. 15(1): 66
      Metabolomics by gas chromatography/mass spectrometry (GC/MS) provides a standardized and reliable platform for understanding small molecule biology. Since 2005, the West Coast Metabolomics Center at the University of California at Davis has collated GC/MS metabolomics data from over 156,000 samples and 2000 studies into the standardized BinBase database. We believe that the observations from these samples will provide meaningful insight to biologists and that our data treatment and webtool will provide insight to others who seek to standardize disparate metabolomics studies. We here developed an easy-to-use query interface, BinDiscover, to enable intuitive, rapid hypothesis generation for biologists based on these metabolomic samples. BinDiscover creates observation summaries and graphics across a broad range of species, organs, diseases, and compounds. Throughout the components of BinDiscover, we emphasize the use of ontologies to aggregate large groups of samples based on the proximity of their metadata within these ontologies. This adjacency allows for the simultaneous exploration of entire categories such as "rodents", "digestive tract", or "amino acids". The ontologies are particularly relevant for BinDiscover's ontologically grouped differential analysis, which, like other components of BinDiscover, creates clear graphs and summary statistics across compounds and biological metadata. We exemplify BinDiscover's extensive applicability in three showcases across biological domains.
    Keywords:  Gas chromatography; Mass spectrometry; Meta-analysis; Metabolomics; Ontologies
  4. Nat Commun. 2023 07 17. 14(1): 4263
      A lipidome comprises thousands of lipid species, many of which are isomers and isobars. Liquid chromatography-tandem mass spectrometry (LC-MS/MS), although widely used for lipidomic profiling, faces challenges in differentiating lipid isomers. Herein, we address this issue by leveraging the orthogonal separation capabilities of hydrophilic interaction liquid chromatography (HILIC) and trapped ion mobility spectrometry (TIMS). We further integrate isomer-resolved MS/MS methods onto HILIC-TIMS, which enable pinpointing double bond locations in phospholipids and sn-positions in phosphatidylcholine. This system profiles phospholipids at multiple structural levels with short analysis time (<10 min per LC run), high sensitivity (nM detection limit), and wide coverage, while data analysis is streamlined using a home-developed software, LipidNovelist. Notably, compared to our previous report, the system doubles the coverage of phospholipids in bovine liver and reveals uncanonical desaturation pathways in RAW 264.7 macrophages. Relative quantitation of the double bond location isomers of phospholipids and the sn-position isomers of phosphatidylcholine enables the phenotyping of human bladder cancer tissue relative to normal control, which would be otherwise indistinguishable by traditional profiling methods. Our research offers a comprehensive solution for lipidomic profiling and highlights the critical role of isomer analysis in studying lipid metabolism in both healthy and diseased states.
  5. J Pharm Biomed Anal. 2023 Jul 17. pii: S0731-7085(23)00363-1. [Epub ahead of print]234 115594
      This article describes the development and validation of a liquid-chromatography coupled with tandem mass spectrometry (LC-MS/MS) assay for the simultaneous quantitation of the BRAF inhibitors dabrafenib and encorafenib, and semi-quantitation of their major metabolites (i.e., carboxy-dabrafenib, desmethyl-dabrafenib, hydroxy-dabrafenib, M42.5A) in human plasma. Analytes were extracted from human plasma by protein precipitation, followed by reversed phase high-performance liquid chromatography. Analyte detection was performed using tandem mass spectrometry with heated electrospray ionization operating in positive ion mode. The assay was validated in accordance with the current U.S. Food and Drug Administration Guidance on Bioanalytical Method Validation. Results showed that measurements were both accurate (94.6-112.0 %) and precise (within-run: 1.9-3.4 %; between-run: 1.7-12.0 %) spanning a concentration range of 5 to 2000 ng/mL for dabrafenib and 10 to 4000 ng/mL for encorafenib. Recoveries for these analytes were consistent with mean values ranging from 85.6 % to 90.9 %. The mean internal standard-normalized matrix factors for each drug ranged between 0.87 and 0.98 and were found to be precise (% RSD <6.4 %). Dabrafenib and encorafenib were stable in the final extract and in human plasma held under various storage conditions. The metabolites also passed the validation criteria for precision and selectivity. Finally, the clinical applicability of the assay was confirmed by (semi-)quantitation of all six analytes in plasma samples from cancer patients receiving standard-of-care treatment with dabrafenib and encorafenib. Reproducibility of the measured analyte concentrations in study samples was confirmed successfully by incurred sample reanalysis. In conclusion, this sensitive LC-MS/MS assay has been validated successfully and is suitable for therapeutic drug monitoring of dabrafenib and encorafenib and clinical pharmacokinetic studies with these BRAF inhibitors.
    Keywords:  BRAF inhibitor; Dabrafenib; Encorafenib; LC–MS/MS; Plasma; Therapeutic drug monitoring
  6. Res Sq. 2023 Jul 06. pii: [Epub ahead of print]
      Liquid Chromatography Mass Spectrometry (LC-MS) is a powerful method for profiling complex biological samples. However, batch effects typically arise from differences in sample processing protocols, experimental conditions and data acquisition techniques, significantlyimpacting the interpretability of results. Correcting batch effects is crucial for the reproducibility of proteomics research, but current methods are not optimal for removal of batch effects without compressing the genuine biological variation under study. We propose a suite of Batch Effect Removal Neural Networks (BERNN) to remove batch effects in large LC-MS experiments, with the goal of maximizing sample classification performance between conditions. More importantly, these models must efficiently generalize in batches not seen during training. Comparison of batch effect correction methods across three diverse datasets demonstrated that BERNN models consistently showed the strongest sample classification performance. However, the model producing the greatest classification improvements did not always perform best in terms of batch effect removal. Finally, we show that overcorrection of batch effects resulted in the loss of some essential biological variability. These findings highlight the importance of balancing batch effect removal while preserving valuable biological diversity in large-scale LC-MS experiments.
  7. J Am Soc Mass Spectrom. 2023 Jul 18.
      Untargeted separation of isomeric and isobaric species in mass spectrometry imaging (MSI) is challenging. The combination of ion mobility spectrometry (IMS) with MSI has emerged as an effective strategy for differentiating isomeric and isobaric species, which substantially enhances the molecular coverage and specificity of MSI experiments. In this study, we have implemented nanospray desorption electrospray ionization (nano-DESI) MSI on a trapped ion mobility spectrometry (TIMS) mass spectrometer. A new nano-DESI source was constructed, and a specially designed inlet extension was fabricated to accommodate the new source. The nano-DESI-TIMS-MSI platform was evaluated by imaging mouse brain tissue sections. We achieved high ion mobility resolution by utilizing three narrow mobility scan windows that covered the majority of the lipid molecules. Notably, the mobility resolution reaching up to 300 in this study is much higher than the resolution obtained in our previous study using drift tube IMS. High-resolution TIMS successfully separated lipid isomers and isobars, revealing their distinct localizations in tissue samples. Our results further demonstrate the power of high-mobility-resolution IMS for unraveling the complexity of biomolecular mixtures analyzed in MSI experiments.
    Keywords:  high mobility resolution; lipid isomers; mass spectrometry imaging; nanospray desorption electrospray ionization (nano-DESI); trapped ion mobility spectrometry (TIMS)
  8. Anal Bioanal Chem. 2023 Jul 19.
      Amino acid analysis (AAA) can be used for absolute quantitation of standard peptides after acid hydrolysis using 6 M HCl. Obtained individual amino acids can then be quantified by liquid chromatography-mass spectrometry (LC-MS). Achieving baseline separation of non-derivatized amino acids is challenging when reversed-phase (RP) chromatography is used. Several derivatization methods are commonly utilized to address this issue; however, derivatization has several drawbacks, such as derivative instability and lack of reproducibility. Currently, separation of non-derivatized amino acids is typically done using HILIC, but HILIC has problems of poor reproducibility and long column equilibration times. We developed a method to quantify non-derivatized amino acids, including methionine and cysteine, from peptide hydrolysates by RP-LC-MS without special pre-treatment of the samples. Samples were spiked with certified isotopically labeled (13C- and/or 15N-) amino acids as internal standards. The amino acids released from acid hydrolysis were then analyzed by RP-UPLC-MRM-MS and quantified using the analyte/internal standard chromatographic peak area ratios. Peptide quantitation was based on the sum of the individual amino acid concentrations from the known peptide sequences. The resulting method did not require derivatization, used standard C18-based reversed-phase liquid chromatography, did not require external calibration, was robust, and was able to quantify all 17 amino acids for which we had internal standards, including the sulfur-containing amino acids, cysteine and methionine, in their respective oxidized forms. This simple and robust method enabled the absolute quantitation of standard peptides using only acid hydrolysis and a standard RP-UPLC-MRM-MS setup.
    Keywords:  Amino acid analysis (AAA); Hydrochloric acid hydrolysis; LC-MRM-MS; Peptide quantification; Stable isotope-labeled internal standards
  9. Anal Bioanal Chem. 2023 Jul 19.
      Lipidomics investigates the composition and function of lipids, typically employing blood or tissue samples as the primary study matrices. Hair has recently emerged as a potential complementary sample type to identify biomarkers in early disease stages and retrospectively document an individual's metabolic status due to its long detection window of up to several months prior to the time of sampling. However, the limited coverage of lipid profiling presented in previous studies has hindered its exploitation. This study aimed to evaluate the lipid coverage of hair using an untargeted liquid chromatography-high-resolution mass spectrometry lipidomics platform. Two distinct three-step exhaustive extraction experiments were performed using a hair metabolomics one-phase extraction technique that has been recently optimized, and the two-phase Folch extraction method which is recognized as the gold standard for lipid extraction in biological matrices. The applied lipidomics workflow improved hair lipid coverage, as only 99 species could be annotated using the one-phase extraction method, while 297 lipid species across six categories were annotated with the Folch method. Several lipids in hair were reported for the first time, including N-acyl amino acids, diradylglycerols, and coenzyme Q10. The study suggests that hair lipids are not solely derived from de novo synthesis in hair, but are also incorporated from sebum and blood, making hair a valuable matrix for clinical, forensic, and dermatological research. The improved understanding of the lipid composition and analytical considerations for retrospective analysis offers valuable insights to contextualize untargeted hair lipidomic analysis and facilitate the use of hair in translational studies.
    Keywords:  Data interpretation; Extraction methods; Hair; Metabolomics; Profiling; Sample preparation
  10. Anal Bioanal Chem. 2023 Jul 15.
      Non-target screening with LC/IMS/HRMS is increasingly employed for detecting and identifying the structure of potentially hazardous chemicals in the environment and food. Structural assignment relies on a combination of multidimensional instrumental methods and computational methods. The candidate structures are often isomeric, and unfortunately, assigning the correct structure among a number of isomeric candidate structures still is a key challenge both instrumentally and computationally. While practicing non-target screening, it is usually impossible to evaluate separately the limitations arising from (1) the inability of LC/IMS/HRMS to resolve the isomeric candidate structures and (2) the uncertainty of in silico methods in predicting the analytical information of isomeric candidate structures due to the lack of analytical standards for all candidate structures. Here we evaluate the feasibility of structural assignment of isomeric candidate structures based on in silico-predicted retention time and database collision cross-section (CCS) values as well as based on matching the empirical analytical properties of the detected feature with those of the analytical standards. For this, we investigated 14 candidate structures corresponding to five features detected with LC/HRMS in a spiked surface water sample. Considering the predicted retention times and database CCS values with the accompanying uncertainty, only one of the isomeric candidate structures could be deemed as unlikely; therefore, the annotation of the LC/IMS/HRMS features remained ambiguous. To further investigate if unequivocal annotation is possible via analytical standards, the reversed-phase LC retention times and low- and high-resolution ion mobility spectrometry separation, as well as high-resolution MS2 spectra of analytical standards were studied. Reversed-phase LC separated the highest number of candidate structures while low-resolution ion mobility and high-resolution MS2 spectra provided little means for pinpointing the correct structure among the isomeric candidate structures even if analytical standards were available for comparison. Furthermore, the question arises which prediction accuracy is required from the in silico methods to par the analytical separation. Based on the experimental data of the isomeric candidate structures studied here and previously published in the literature (516 retention time and 569 CCS values), we estimate that to reduce the candidate list by 95% of the structures, the confidence interval of the predicted retention times would need to decrease to below 0.05 min for a 15-min gradient while that of CCS values would need to decrease to 0.15%. Hereby, we set a clear goal to the in silico methods for retention time and CCS prediction.
    Keywords:  Cyclic IMS; High-resolution mass spectrometry; Liquid chromatography; Machine learning; Non-targeted analysis; Water analysis
  11. Bio Protoc. 2023 Jul 05. 13(13): e4773
      Non-alcoholic steatohepatitis (NASH) is a condition characterized by inflammation and hepatic injury/fibrosis caused by the accumulation of ectopic fats in the liver. Recent advances in lipidomics have allowed the identification and characterization of lipid species and have revealed signature patterns of various diseases. Here, we describe a lipidomics workflow to assess the lipid profiles of liver homogenates taken from a NASH mouse model. The protocol described below was used to extract and analyze the metabolites from the livers of mice with NASH by liquid chromatography-mass spectrometry (LC-MS); however, it can be applied to other tissue homogenate samples. Using this method, over 1,000 species of lipids from five classes can be analyzed in a single run on the LC-MS. Also, partial elucidation of the identity of neutral lipid (triacylglycerides and diacylglycerides) aliphatic chains can be performed with this simple LC-MS setup. Key features Over 1,000 lipid species (sphingolipids, cholesteryl esters, neutral lipids, phospholipids, fatty acids) are analyzed in one run. Analysis of liver lipids in non-alcoholic steatohepatitis (NASH) mouse model. Normal-phase chromatography coupled to a triple quadrupole mass spectrometer.
    Keywords:  Cholesteryl esters; Fatty acids; Glycerolipids; LC-MS; Lipidomics; Liver; Phospholipids; Sphingolipids
  12. Crit Rev Anal Chem. 2023 Jul 16. 1-16
      Bioactive compounds in functional foods, medicinal plants and others are considered attractive value-added molecules based on their wide range of bioactivity. It is clear that an important role is occupied by polyphenol, phenolic compounds and others. Urine is an effective biofluid to evaluate and monitor alterations in homeostasis and other processes related to metabolism. The current review provides a detailed description of the formation of urine in human body, various aspects relevant to sampling and analysis of urinary metabolites before presenting recent developments leveraging on metabolite profiling of urine. For the profiling of small molecules in urine, advancement of liquid chromatography mass tandem spectrometry (LC/MS/MS), establishment of standardized chemical fragmentation libraries, computational resources, data-analysis approaches with pattern recognition tools have made it an attractive option. The profiling of urinary metabolites gives an overview of the biomarkers associated with the diet and evaluates its biological effects. Metabolic pathways such as glycolysis, tricarboxylic acid cycle, amino acid metabolism, energy metabolism, purine metabolism and others can be evaluated. Finally, a combination of metabolite profiling with chemical standardization and bioassay in functional food and medicinal plants will likely lead to the identification of new biomarkers and novel biochemical insights.
    Keywords:  Urine; bioactive compounds and functional food and medicinal plants; liquid chromatography tandem mass spectrometry; metabolite profiling
  13. Methods Mol Biol. 2023 ;2687 107-126
      The determination of the concentration of endocannabinoids and related compounds in human plasma has become a matter of interest due to their implication in physiological processes and, thus, their possible relation with physiological conditions or illnesses. The analysis of these compounds though has to be carefully designed as they are found in very low concentrations, and some of them degrade easily once blood is collected. In this chapter, a simple method based on a liquid-liquid extraction and analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) is described to determine the concentration of eight of the most relevant endocannabinoids in plasma.
    Keywords:  2-Arachidonoylglycerol; Endocannabinoids; Liquid chromatography; Liquid-liquid extraction; N-arachidonoylethanolamine; Plasma; Tandem mass spectrometry
  14. Microbiol Resour Announc. 2023 Jul 19. e0039223
      From an animal health perspective, our understanding of the metabolites in rumen fluid across different host species is poorly understood. Here, we present a metabolomic data set generated using hydrophilic interaction liquid chromatography and semi-polar (C18) chromatography methods coupled to high-resolution mass spectrometry of fractionated ovine rumen samples.
    Keywords:  biofluid; metabolomics; ovine; rumen
  15. Talanta. 2023 Jul 11. pii: S0039-9140(23)00669-0. [Epub ahead of print]266(Pt 1): 124918
      Liquid chromatography-mass spectrometry (LC-MS) is currently the gold-standard technique for the analysis of non-volatile small organic molecules. However, one-dimensional liquid chromatography (1D-LC) cannot efficiently deal with mixtures of analytes with different physicochemical properties and, thus, specific chromatographic behaviour. As an alternative, this work proposes a two-dimensional liquid chromatography/high-resolution mass spectrometry (2D-LC-HRMS) approach for the simultaneous analysis of compounds with different polarities. It is based on the combination of hydrophilic interaction liquid chromatography (HILIC) in the first dimension (1D) and reversed-phase chromatography (RPLC) in the second dimension (2D), employing the heart-cutting methodology. The coupling between 1D and 2D was performed by a multiple heart-cutting (MHC) interface equipped with an active solvent modulation (ASM) valve. The aim of the study was the development of a 2D-LC methodology able to (i) acquire the 1D and 2D content by MS in a single analytical run, avoiding the loss of information caused by the MHC algorithm for filling the sampling loops; (ii) overcome the breakthrough problem caused by solvent incompatibility, modifying the 2D gradient during the ASM phase for this purpose. To evaluate the 2D-LC approach, pesticide residue analysis was proposed, selecting 20 pesticides covering a wide range of polarities (log Kow from -3.2 to 4.3) and including some of the so-called single residue method pesticides because of the difficulty of including them in 1D-LC multi-residue methods with satisfactory chromatographic resolution. The proposed strategy was to transfer in a single cut the void volume from the HILIC separation (consisting of the nonpolar pesticides) to the 2D for analysis under RPLC conditions. The developed assembly was assessed in a vegetable matrix (tomato) employing a hybrid QuEChERS/QuPPe sample treatment based on acetonitrile and methanol extraction. The proposed setup may be extended for 2D-LC applications where it is essential to acquire the entire content of both dimensions in a single data file just by coupling a selection valve to the MHC interface.
    Keywords:  Active solvent modulation; Breakthrough; Heart-cutting; Pesticide; Selection valve; Two-dimensional liquid chromatography
  16. Analyst. 2023 Jul 17.
      Metabolites in biological matrices belong to diverse chemical groups, ranging from non-polar long-chain fatty acids to small polar molecules. The goal of untargeted metabolomic analysis is to measure the highest number of metabolites in the sample. Nevertheless, from an analytical point of view, no single technique can measure such a broad spectrum of analytes. Therefore, we selected a method based on GC-MS and LC-MS with two types of stationary phases for the untargeted profiling of gastrointestinal stromal tumours. The procedure was applied to GIST xenograft samples (n = 71) representing four different mutation models, half of which were treated with imatinib. We aimed to verify the method coverage and advantages of applying each technique. RP-LC-MS measured most metabolites due to a significant fraction of lipid components of the tumour tissue. What is unique and worth noting is that all applied techniques were able to distinguish between different mutation models. However, for detecting imatinib-induced alterations in the GIST metabolome, RP-LC-MS and GC-MS proved to be more relevant than HILIC-LC-MS, resulting in a higher number of significantly changed metabolites in four treated models. Undoubtedly, the inclusion of all mentioned techniques makes the method more comprehensive. Nonetheless, for green chemistry and time and labour saving, we assume that RP-LC-MS and GC-MS analyses are sufficient to cover the global GIST metabolome.
  17. Anal Bioanal Chem. 2023 Jul 19.
      Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.
    Keywords:  Chemical derivatization; Lipidomics; Mass spectrometry imaging; Metabolomics; Proteomics; Single-cell analysis
  18. J Pharm Biomed Anal. 2023 Jun 03. pii: S0731-7085(23)00273-X. [Epub ahead of print]234 115504
      Mycophenolate mofetil (MMF) is a prodrug of mycophenolic acid (MPA) used to prevent rejection in organ transplant patients. The purpose of this study is to develop a sensitive LC-MS/MS method to simultaneously quantify MMF, MPA, and two major metabolites, mycophenolic acid-glucuronide (MPAG) and Acyl-mycophenolic acid-glucuronide (AcMPAG) and applied this method in a pharmacokinetic (PK) and tissue distribution study. A Shimadzu UHPLC system coupled to an AB Sciex QTrap 4000 mass spectrometer was used for the analysis. Protein precipitation with a mixture of methanol: acetonitrile (2:1, v:v) was used to process the plasma samples and tissue samples. Separation was achieved using an Ultra Biphenyl 5 µm column (100 × 2.1 mm) with 0.1% formic acid in water (A) and acetonitrile (B) as the mobile phases. Quantification analysis was performed under positive ionization mode using the multiple reaction monitoring (MRM) approach. The method was linear in the range of 1.22 - 1250.00 nM for all four analytes with correlation coefficient values > 0.99. The method was reproducible, with intra- and inter-day accuracy ranging from 85.0 ± 11.2-108.3 ± 6.50 for all analytes in both plasma, liver and intestine homogenates. The extraction recovery and matrix effect of plasma sample using a mixture methanol/acetonitrile (2:1, V:V) can achieve an acceptable range (<20%), but extraction recovery and matrix effect of AcMPAG decreased to 64.10 ± 15.42 in the liver and intestine homogenates. The analytes in plasma were found to be stable under bench-top, freeze-thaw, and storage conditions. The validated method was successfully applied to quantify MMF, MPA, MPAG, and AcMPAG in a rat PK study. The PK results showed MPA was the major form exposed in the plasma in rats after oral administration of MMF, but the major metabolites in the rat's tissue disposition were MPAG.
    Keywords:  LC-MS/MS; Metabolites; Mycophenolate mofetil; Mycophenolic acid; Pharmacokinetics; Tissue distribution
  19. J Pharm Biomed Anal. 2023 May 24. pii: S0731-7085(23)00253-4. [Epub ahead of print]234 115484
      Polycystic ovary syndrome (PCOS) is a common endocrine disorder that causes reproductive hormones imbalance, missed periods, infertility and distributed steroidogenesis. Reportedly, during PCOS, the endogenous levels of P4 (Progesterone), 17OHP4 (17-α hydroxy progesterone), and T4 (Testosterone) were significantly altered. Thus, quantification of steroid biomarkers involved in the steroidogenesis pathway of PCOS, such as P4, 17OHP4, and T4, holds significant importance. One important drawback of current methods is steroid metabolome traceability. Without adequate traceability, the findings of these techniques will be less reliable for identifying P4, 17OHP4, and T4. These methods also need a high sample size, especially for the most important biomarker that initiates steroidogenesis. To address these challenges, we require a new liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for steroid biomarker analysis. Herein the present work, using validated LC-MS/MS, PCOS biomarkers were measured and compared between normal control rats and PCOS-induced rats before and after analyte administration. The experiment utilized an isocratic separation method employing an analytical C18 column. The mobile phase consisted of acetonitrile (ACN) and aqueous 0.1% formic acid (FA) in a ratio of 90:10 (v/v). The plasma samples were processed with protein precipitation (PPT) followed by the liquid-liquid extraction (LLE) method. The lower limit of quantification (LLOQ) was 0.5 ng/mL in plasma. According to USFDA criteria, the method's systematic validation took into account linearity (r2 > 0.99), accuracy and precision of intra- and inter-batch measurements, stability, biomarker recovery (60-85%) and matrix effect (<± 15%), all of which were determined to be within range ( ± 15%). The pharmacokinetic data showed that, as compared to normal rats, PCOS-induced animals had significantly higher Cmax values for 17OHP4 and T4 (∼2 fold), while lower Cmax values for P4 (∼2 fold). The present work is novel and provides scientific information to explore systematic processes involved in steroidogenesis and boost clinical applicability for PCOS therapy.
    Keywords:  17-α hydroxy progesterone; Biomarker; LC-MS/MS diagnostic method; Letrozole; Metabolite; PCOS; Progesterone; Steroidogenesis; Testosterone
  20. Curr Opin Chem Biol. 2023 Jul 18. pii: S1367-5931(23)00108-4. [Epub ahead of print]76 102370
      The objective of this review is to provide a comprehensive summary of the latest methodological advancements and emerging patterns in utilizing lipidomics in clinical research.In this review, we assess the recent advancements in lipidomics methodologies that exhibit high levels of selectivity and sensitivity, capable of generating numerous molecular lipid species from limited quantities of biological matrices. The reviewed studies demonstrate that molecular lipid signatures offer new opportunities for precision medicine by providing sensitive diagnostic tools for disease prediction and monitoring. Moreover, the latest innovations in microsampling techniques have the potential to make a substantial contribution to clinical lipidomics. The review also shows that more work is needed to harmonize results across diverse lipidomics platforms and avoid significant errors in analysis and reporting. The increased implementation of internal standards and standard reference materials in analytical workflows will aid in this direction.
    Keywords:  Biomarkers; Human health; Lipidomics; Mass spectrometry; Microsampling
  21. Chem Res Toxicol. 2023 Jul 18.
      Smoking is a risk factor for bladder cancer (BC), although the specific chemicals responsible for BC remain uncertain. Considerable research has focused on aromatic amines (AAs), including o-toluidine (o-tol), o-anisidine (o-anis), 2-naphthylamine (2-NA), and 4-aminobiphenyl (4-ABP), which are linked to human BC based on elevated BC incidence in occupationally exposed factory workers. These AAs arise at nanogram levels per combusted cigarette. The unambiguous identification of AAs, particularly low-molecular-weight monocyclic AAs in tobacco smoke extracts, by liquid chromatography-mass spectrometry (LC-MS) is challenging due to their poor performance on reversed-phase columns and co-elution with isobaric interferences from the complex tobacco smoke matrix. We employed a tandem liquid-liquid and solid-phase extraction method to isolate AAs from the basic fraction of tobacco smoke condensate (TSC) and utilized high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to high-resolution accurate mass (HRAM) Orbitrap LC-MS2 to assay AAs in TSC. The employment of FAIMS greatly reduced sample complexity by removing precursor co-isolation interfering species at the MS1 scan stage, resulting in dramatically improved signal-to-noise of the precursor ions and cleaner, high-quality MS2 spectra for unambiguous identification and quantification of AAs in TSC. We demonstrate the power of LC/FAIMS/MS2 by characterizing and quantifying two low-molecular-weight carcinogenic AAs, o-tol and o-anis, in TSC, using stable isotopically labeled internal standards. These results demonstrate the power of FAIMS in trace-level analyses of AA carcinogens in the complex tobacco smoke matrix.
  22. Anal Chem. 2023 Jul 19.
      Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) is a powerful analytical technique that provides spatially preserved detection and quantification of analytes in tissue specimens. However, clinical translation still requires improved throughput, precision, and accuracy. To accomplish this, we created "Chemical QuantArray", a gelatin tissue microarray (TMA) mold filled with serial dilutions of isotopically labeled endogenous metabolite standards. The mold is then cryo-sectioned onto a tissue homogenate to produce calibration curves. To improve precision and accuracy, we automatically remove pixels outside of each TMA well and investigated several intensity normalizations, including the utilization of a second stable isotope internal standard (IS). Chemical QuantArray enables the quantification of several endogenous metabolites over a wide dynamic range and significantly improve over current approaches. The technique reduces the space needed on the MALDI slides for calibration standards by approximately 80%. Furthermore, removal of empty pixels and normalization to an internal standard or matrix peak provided precision (<20% RSD) and accuracy (<20% DEV). Finally, we demonstrate the applicability of Chemical QuantArray by quantifying multiple purine metabolites in 14 clinical tumor specimens using a single MALDI slide. Chemical QuantArray improves the analytical characteristics and practical feasibility of MALDI-MSI metabolite quantification in clinical and translational applications.
  23. J Sep Sci. 2023 Jul 19. e2300351
      This work describes a comprehensive achiral × chiral two-dimensional liquid chromatography separation for enantioselective amino acid analysis coupled to electrospray ionization-tandem mass spectrometry detection using data-independent acquisition. Flow splitting after the first and second dimension separation was utilized for volumetric flow reduction and for enabling a multi-detector approach (with ultraviolet, fluorescence, charged aerosol, and MS detection), respectively. Derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate provided a chromophore, a fluorophore, and an efficient mass tag for efficient ionization in positive electrospray ionization-mass spectrometry. Chiral columns often have limitations in terms of their chemoselectivity, which may be a problem when complex sample mixtures with structurally related compounds need to be separated. It can be alleviated by a reversed-phase×chiral two-dimensional-liquid chromatography setup, in which the first dimension provides the chemoselectivity and a chiral tandem column constituted of quinine-carbamate derived weak anion-exchanger and zwitterionic ion-exchanger in the second dimension separation of D- and L-amino acid enantiomers. The method was used to control the stereointegrity of the therapeutic peptide octreotide. After hydrolysis, all amino acid constituents were detected with the correct configuration and composition. Some options for flow splitting and integration of destructive detectors in the first dimension separation are outlined.
    Keywords:  chiral separation; flow splitting; mass-tag; multidimensional liquid chromatography; untargeted analysis
  24. Anal Chim Acta. 2023 Sep 15. pii: S0003-2670(23)00794-8. [Epub ahead of print]1274 341573
      Systematic selection of mobile phase and column chemistry type can be critical for achieving optimal chromatographic separation, high sensitivity, and low detection limits in liquid chromatography electrospray high resolution mass spectrometry (LC/MS). However, the selection process is challenging for non-targeted screening where the compounds of interest are not preselected nor available for method optimization. To provide general guidance, twenty different mobile phase compositions and four columns were compared for the analysis of 78 compounds with a wide range of physicochemical properties (logP range from -1.46 to 5.48), and analyte sensitivity was compared between methods. The pH, additive type, column, and organic modifier had significant effects on the analyte response factors, and acidic mobile phases (e.g. 0.1% formic acid) yielded highest sensitivity. In some cases, the effect was attributable to the difference in organic modifier content at the time of elution, depending on the mobile phase and column chemistry. Based on these findings, 0.1% formic acid, 0.1% ammonia and 5.0 mM ammonium fluoride were further evaluated for their performance in non-targeted LC/ESI/HRMS analysis of wastewater treatment plan influent and effluent, using a data dependent MS2 acquisition and two different data processing workflows (MS-DIAL, patRoon 2.1) to compare number of detected features and sensitivity. Both data-processing workflows indicated that 0.1% formic acid yielded the highest number of features in full scan spectrum (MS1), as well as the highest number of features that triggered fragmentation spectra (MS2) when dynamic exclusion was used.
    Keywords:  Data dependent acquisition; Identification of unknowns; Ionization efficiency; Limit of detection; Method optimization
  25. Nat Protoc. 2023 Jul 21.
      Mass spectrometry imaging (MSI) enables the chemical mapping of molecules and elements in a label-free, high-throughput manner. Because this approach can be accomplished rapidly, it also enables chemical changes to be monitored. Here, we describe a protocol for MSI with subcellular spatial resolution. This is achieved by using a microlensed fiber, which is made by grinding an optical fiber. It is a universal and economic technique that can be adapted to most laser-based mass spectrometry methods. In this protocol, the output of laser radiation from the microlensed fiber causes laser ablation of the sample, and the resulting plume is mass spectrometrically analyzed. The microlensed fiber can be used with matrix-assisted laser desorption ionization, laser desorption ionization, laser ablation electrospray desorption ionization and laser ablation inductively coupled plasma, in each case to achieve submicroscale imaging of single cells and biological tissues. This report provides a detailed introduction of the microlensed fiber design and working principles, sample preparation, microlensed fiber ion source setup and multiple MSI platforms with different kinds of mass spectrometers. A researcher with a little background (such as a trained graduate student) is able to complete all the steps for the experimental setup in ~2 h, including fiber test, laser coupling and ion source modification. The imaging time spent mainly depends on the size of the imaging area. It is suggested that most existing laser-based MSI platforms, especially atmospheric pressure applications, can achieve breakthroughs in spatial resolution by introducing a microlensed fiber module.
  26. Talanta. 2023 Jul 12. pii: S0039-9140(23)00672-0. [Epub ahead of print]266(Pt 1): 124921
      Oxylipins - involved in inflammatory processes - are reported in several diseases, in biological, pharmacological, and physiological fields. To face the structural complexity of oxylipins, the study of isomers and isobars species relied on Selected Reaction Monitoring (SRM) and Multiple Reaction Monitoring (MRM) in tandem mass spectrometry such as triple quadrupole, quadrupole-Time of Flight (TOF). Unfortunately, false positive signals in cellular matrix could occur using MRM or SRM mode since the MS/MS spectrum of each molecule is not acquired with the previous mode to help molecule confirmation. Using the versatile ability of LTQ-Orbitrap® Velos Pro mass spectrometer, we developed a novel method based on data dependent acquisition (DDA) workflow for oxylipins analysis. To reach sufficient data points per peak and a better sensitivity to quantify oxylipins traces, an optimization of the acquisition frequency was carried out both on linear trap and Orbitrap analyzers. A segmentation of the chromatographic profile and an optimization of the collision energies by HCD (higher energy collision dissociation) for each eicosanoid increased the acquisition frequency significantly and the detection threshold: around 2 pg for some prostanoids and 0.02-2 pg for some leukotrienes and oxidized species. We validated our method in terms of specificity (RSD <10%), sensitivity, accuracy and precision. The intra and inter-day accuracy were between 86.56% and 114.93%. Besides, a relative standard deviation less than 15% as intra- and inter-day precision were obtained for almost all molecules. A linear range between 2.5 and 12,500 pg was reached. DDA approach on LTQ-Orbitrap® constitutes an alternative to MRM mode on triple quadrupole for eicosanoids quantification in complex matrices. Finally, this method helped us to compare for the first time the amount of prostanoids released by J774 and THP-1 macrophages under lipopolysaccharide (LPS) stimulation.
    Keywords:  Data dependent acquisition (DDA); J774 and THP-1 macrophages; Mass spectrometry (LTQ-Orbitrap® Velos Pro); Oxylipins; Reverse phase liquid chromatography; Selected reaction monitoring (SRM)
  27. Anal Chim Acta. 2023 Sep 15. pii: S0003-2670(23)00799-7. [Epub ahead of print]1274 341578
      Although interest in characterizing DNA damage by means of DNA adductomics has substantially grown, the field of DNA adductomics is still in its infancy, with room for optimization of methods for sample analysis, data processing and DNA adduct identification. In this context, the first objective of this study was to evaluate the use of hydrophilic interaction (HILIC) vs. reversed phase liquid chromatography (RPLC) coupled to high resolution mass spectrometry (HRMS) and thermal acidic vs. enzymatic hydrolysis of DNA followed by DNA adduct purification and enrichment using solid-phase extraction (SPE) or fraction collection for DNA adductome mapping. The second objective was to assess the use of total ion count (TIC) and median intensity (MedI) normalization compared to QC (quality control), iQC (internal QC) and quality control-based robust locally estimated scatterplot smoothing (LOESS) signal correction (QC-RLSC) normalization for processing of the acquired data. The results demonstrate that HILIC compared to RPLC allowed better modeling of the tentative DNA adductome, particularly in combination with thermal acidic hydrolysis and SPE (more valid models, with an average Q2(Y) and R2(Y) of 0.930 and 0.998, respectively). Regarding the need for data normalization and the management of (limited) system instability and signal drift, QC normalization outperformed TIC, MedI, iQC and LOESS normalization. As such, QC normalization can be put forward as the default data normalization strategy. In case of momentous signal drift and/or batch effects however, comparison to other normalization strategies (like e.g. LOESS) is recommended. In future work, further optimization of DNA adductomics may be achieved by merging of HILIC and RPLC datasets and/or application of 2D-LC, as well as the inclusion of Schiff base stabilization and/or fraction collection in the thermal acidic hydrolysis-SPE sample preparation workflow.
    Keywords:  DNA adduct purification; Discriminant analysis; Hydrophilic interaction liquid chromatography; Normalization; Reversed phase liquid chromatography
  28. J Agric Food Chem. 2023 Jul 19.
      Lotus japonicus is a leguminous model plant used to gain insight into plant physiology, stress response, and especially symbiotic plant-microbe interactions, such as root nodule symbiosis or arbuscular mycorrhiza. Responses to changing environmental conditions, stress, microbes, or insect pests are generally accompanied by changes in primary and secondary metabolism to account for physiological needs or to produce defensive or signaling compounds. Here we provide an overview of the primary and secondary metabolites identified in L. japonicus to date. Identification of the metabolites is mainly based on mass spectral tags (MSTs) obtained by gas chromatography linked with tandem mass spectrometry (GC-MS/MS) or liquid chromatography-MS/MS (LC-MS/MS). These MSTs contain retention index and mass spectral information, which are compared to databases with MSTs of authentic standards. More than 600 metabolites are grouped into compound classes such as polyphenols, carbohydrates, organic acids and phosphates, lipids, amino acids, nitrogenous compounds, phytohormones, and additional defense compounds. Their physiological effects are briefly discussed, and the detection methods are explained. This review of the exisiting literature on L. japonicus metabolites provides a valuable basis for future metabolomics studies.
    Keywords:  Lotus japonicus; mass spectral tags; metabolomics; phytohormones; plant−microbe interactions; primary metabolites; secondary metabolites