bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒03‒05
24 papers selected by
Sofia Costa

  1. Se Pu. 2023 Mar;41(3): 274-280
      The detection of paralytic shellfish toxins in human biological matrices is important for the diagnosis and treatment of food poisoning caused by them. An ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was established for the determination of 14 paralytic shellfish toxins in plasma and urine. The effect of solid phase extraction (SPE) cartridges was also investigated and the pretreatment and chromatographic conditions were optimized. Under these optimal conditions, 0.2 mL water, 0.4 mL methanol, and 0.6 mL acetonitrile were successively added to plasma and urine samples for extraction. The supernatants from plasma extraction were subjected to an UHPLC-MS/MS analysis, whereas the supernatants from urine extraction were further purified using polyamide (PA) SPE cartridges and then analyzed by UHPLC-MS/MS. Chromatographic separation was conducted on a Poroshell 120 HILIC-Z column (100 mm×2.1 mm, 2.7 μm) with a flow rate of 0.5 mL/min. The mobile phase was 0.1% (v/v) formic acid aqueous solution containing 5 mmoL/L ammonium formate and acetonitrile containing 0.1% (v/v) formic acid. The analytes were detected in the multiple reaction monitoring (MRM) mode after being ionized by an electrospray ion (ESI) in positive and negative modes. Quantitation of the target compounds was performed using the external standard method. Under the optimal conditions, the method showed good linearity in the range of 0.24-84.06 μg/L, with correlation coefficients greater than 0.995. The limits of quantification (LOQs) for the plasma and urine samples were 1.68-12.04 ng/mL and 4.80-34.4 ng/mL, respectively. The average recoveries for all the compounds were 70.4%-123.4% at spiked levels of 1, 2, and 10 times the LOQs, the intra-day precisions were 2.3%-19.1% and the inter-day precisions were 5.0%-16.0%. The established method was used to determine the target compounds in the plasma and urine from mice intraperitoneally injected with 14 shellfish toxins. All 14 toxins were detected in the 20 urine and 20 plasma samples, with contents of 19.40-55.60 μg/L and 8.75-13.86 μg/L, respectively. The method is simple, sensitive, and only requires a small amount of sample. Therefore, it is highly suitable for the rapid detection of paralytic shellfish toxins in plasma and urine.
    Keywords:  paralytic shellfish toxins; plasma; ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS); urine
  2. Metabolomics. 2023 Mar 01. 19(3): 15
      INTRODUCTION: There is still no community consensus regarding strategies for data quality review in liquid chromatography mass spectrometry (LC-MS)-based untargeted metabolomics. Assessing the analytical robustness of data, which is relevant for inter-laboratory comparisons and reproducibility, remains a challenge despite the wide variety of tools available for data processing.OBJECTIVES: The aim of this study was to provide a model to describe the sources of variation in LC-MS-based untargeted metabolomics measurements, to use it to build a comprehensive curation pipeline, and to provide quality assessment tools for data quality review.
    METHODS: Human serum samples (n=392) were analyzed by ultraperformance liquid chromatography coupled to high-resolution mass spectrometry (UPLC-HRMS) using an untargeted metabolomics approach. The pipeline and tools used to process this dataset were implemented as part of the open source, publicly available TidyMS Python-based package.
    RESULTS: The model was applied to understand data curation practices used by the metabolomics community. Sources of variation, which are often overlooked in untargeted metabolomic studies, were identified in the analysis. New tools were used to characterize certain types of variations.
    CONCLUSION: The developed pipeline allowed confirming data robustness by comparing the experimental results with expected values predicted by the model. New quality control practices were introduced to assess the analytical quality of data.
    Keywords:  Data curation; Liquid chromatography; Mass spectrometry; Quality control practices
  3. bioRxiv. 2023 Feb 21. pii: 2023.02.20.529280. [Epub ahead of print]
      Cardinal v3 is an open source software for reproducible analysis of mass spectrometry imaging experiments. A major update from its previous versions, Cardinal v3 supports most mass spectrometry imaging workflows. Its analytical capabilities include advanced data processing such as mass re-calibration, advanced statistical analyses such as single-ion segmentation and rough annotation-based classification, and memory-efficient analyses of large-scale multi-tissue experiments.
  4. Biol Pharm Bull. 2023 ;46(3): 455-463
      CYP3A4, which contributes to the metabolism of more than 30% of clinically used drugs, exhibits high variation in its activity; therefore, predicting CYP3A4 activity before drug treatment is vital for determining the optimal dosage for each patient. We aimed to develop and validate an LC-tandem mass spectrometry (LC-MS/MS) method that simultaneously measures the levels of CYP3A4 activity-related predictive biomarkers (6β-hydroxycortisol (6β-OHC), cortisol (C), 1β-hydroxydeoxycholic acid (1β-OHDCA), and deoxycholic acid (DCA)). Chromatographic separation was achieved using a YMC-Triart C18 column and a gradient flow of the mobile phase comprising deionized water/25% ammonia solution (100 : 0.1, v/v) and methanol/acetonitrile/25% ammonia solution (50 : 50 : 0.1, v/v/v). Selective reaction monitoring in the negative-ion mode was used for MS/MS, and run times of 33 min were used. All analytes showed high linearity in the range of 3-3000 ng/mL. Additionally, their concentrations in urine samples derived from volunteers were analyzed via treatment with deconjugation enzymes, ignoring inter-individual differences in the variation of other enzymatic activities. Our method satisfied the analytical validation criteria under clinical conditions. Moreover, the concentrations of each analyte were quantified within the range of calibration curves for all urine samples. The conjugated forms of each analyte were hydrolyzed to accurately examine CYP3A4 activity. Non-invasive urine sampling employed herein is an effective alternative to invasive plasma sampling. The analytically validated simultaneous quantification method developed in this study can be used to predict CYP3A4 activity in precision medicine and investigate the potential clinical applications of CYP3A4 biomarkers (6β-OHC/C and 1β-OHDCA/DCA ratios).
    Keywords:  CYP3A4; LC-tandem mass spectrometry; biomarker; pharmacokinetics; urine
  5. Drug Test Anal. 2023 Feb 27.
      In the present study, the application and evaluation of Girard Reagent T (GRT) derivatization for the simultaneous detection and significantly important identification of different phase II methenolone and mesterolone metabolites by LC-MS/(MS) are presented. For the LC-MS analysis of target analytes two complementary isolation methods were developed; a derivatization and shoot method in which native urine is diluted with derivatization reagent and is injected directly to LC-MS and a liquid liquid extraction method, using ethyl acetate at pH 4.5, for the effective isolation of both sulfate and glucuronide metabolites of the named steroids as well as of their free counterparts. For the evaluation of the proposed protocols, urine samples from methenolone and mesterolone excretion studies were analyzed against at least one sample from a different excretion study. Retention times, along with product ion ratios, were evaluated according to the WADA TD2021IDCR requirements, in order to determine maximum detection and identification time windows for each metabolite. Established identification windows obtained after LC-MS/(MS) analysis were further compared with those obtained after GC-MS/(MS) analysis of the same samples from the same excretion studies, for the most common analytes monitored by GC-MS/(MS). Full validation was performed for the developed derivatization and shoot method for the identification of methenolone metabolite, 3α-hydroxy-1-methylen-5α-androstan-17-one-3-glucuronide (mth3). Overall, the GRT derivatization presented herein, offers a tool for the simultaneous sensitive detection of free, intact glucuronide and sulfate metabolites by LC-MS/(MS) that enhance significantly the detection and identification time windows of specific methenolone and mesterolone metabolites for doping control analysis.
    Keywords:  Girard’s T derivatization; LC-MS(/MS); doping control; glucuronide metabolites; mesterolone; methenolone; sulfate metabolites
  6. Se Pu. 2023 Mar;41(3): 224-232
      Pesticides are widely used in most agricultural areas to protect food crops but adversely affect ecosystems and human beings. Pesticides have attracted great public concern due to their toxic properties and ubiquitous occurrence in the environment. China is one of the largest users and producers of pesticides globally. However, limited data are available on pesticide exposure in humans, which warrants a method for quantification of pesticides in human samples. In the present study, we validated and developed a comprehensive and sensitive method for the quantification of two phenoxyacetic herbicides, two metabolites of organophosphorus pesticides and four metabolites of pyrethroid pesticides in human urine using 96-well plate solid phase extraction (SPE) coupled with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). For this purpose, a systematic optimization of the chromatographic separation conditions and MS/MS parameters was conducted. Six solvents were optimized for the extraction and clean-up of human urine samples. The targeted compounds in the human urine samples were well separated within 16 min in one analytical run. A 1 mL aliquot of human urine sample was mixed with 0.5 mL sodium acetate buffer (0.2 mol/L) and hydrolyzed by β-glucuronidase enzyme at 37 ℃ overnight. The eight targeted analytes were extracted and cleaned using an Oasis HLB 96-well solid phase plate and eluted with methanol. The separation of the eight target analytes was performed on a UPLC Acquity BEH C18 column (150 mm×2.1 mm, 1.7 μm) with gradient elution using 0.1% (v/v) acetic acid in acetonitrile and 0.1% (v/v) acetic acid in water. The analytes were identified using the multiple reaction monitoring (MRM) mode under negative electrospray ionization (ESI-) and quantified by isotope-labelled analogs. Para-nitrophenol (PNP), 3,5,6-tricholor-2-pyridinol (TCPY) and cis-dichlorovinyl-dimethylcyclopropane carboxylic acid (cis-DCCA) exhibited good linearities ranging from 0.2 to 100 μg/L, and 3-phenoxy benzoic acid (3-PBA), 4-fluoro-3-phenoxy benzoic acid (4F-3PBA), 2,4-dicholorphenoxyacetic acid (2,4-D), trans-dichlorovinyl-dimethylcyclopropane carboxylic acid (trans-DCCA) and 2,4,5-tricholorphenoxyacetic acid (2,4,5-T) showed linearity ranging from 0.1 to 100 μg/L with correlation coefficients all above 0.9993. Method detection limits (MDLs) and method quantification limits (MQLs) of targeted compounds were in the range of 0.02 to 0.07 μg/L and 0.08 to 0.2 μg/L, respectively. The spiked recoveries of target compounds at three levels of 0.5, 5 and 40 μg/L were 91.1% to 110.5%. The inter- and intra-day precisions of targeted analytes were 2.9% to 7.8% and 6.2% to 10%, respectively. This method was applied to the analysis of 214 human urine samples across China. The results showed that all the targeted analytes, except 2,4,5-T, were detected in human urine. The detection rates of TCPY, PNP, 3-PBA, 4F-3PBA, trans-DCCA, cis-DCCA, and 2,4-D were 98.1%, 99.1%, 94.4%, 2.80%, 99.1%, 63.1% and 94.4%, respectively. The median concentration of targeted analytes in a decreasing order were: 2.0 μg/L (TCPY), 1.8 μg/L (PNP), 0.99 μg/L (trans-DCCA), 0.81 μg/L (3-PBA), 0.44 μg/L (cis-DCCA), 0.35 μg/L (2,4-D) and below MDLs (4F-3PBA ). For the first time, we developed a method to extract and purify specific biomarkers of pesticides from human samples based on offline 96-well SPE. This method has the advantages of simple operation, high sensitivity, and high accuracy. Moreover, up to 96 human urine samples were analyzed in one batch. It is suitable for the determination of eight specific pesticides and their metabolites in large sample sizes.
    Keywords:  biomonitoring; internal exposure; metabolites; pesticides; solid phase extraction (SPE); ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); urine
  7. J Am Soc Mass Spectrom. 2023 Feb 28.
      As part of a larger effort to aid in seamless integration of Fourier-based multiplexed ion mobility with a range mass analyzers, we have developed an all-in-one graphical user interface tool for FT-IM-MS data analysis that runs directly within a web browser. This tool, FTflow, accepts mzML files and displays necessary information such as mass spectra and extracted ion chromatograms in order to reconstruct arrival time distributions. It also extracts the corresponding mobility-related information (e.g., Ko and CCS) for each of the target ion populations. Furthermore, input fields for experimental conditions are clearly laid out for users and ease-of-use. With flexibility in mind, the processing scripts and GUI interface are written entirely in Python and allows users the option to modify source code to fit their specific needs. While the intention for this tool is to be a starting point for exploratory analysis of FT-IM-MS data, it has the capability to be adapted for use in more automated data processing pipelines through direct access of core processing routines.
    Keywords:  Fourier transform; graphical user interface (GUI); ion mobility; ion trap; mass spectrometry; multiplexing; signal processing
  8. Ann Lab Med. 2023 Jul 01. 43(4): 345-354
      Background: Serum C-peptide results from various routine methods used in China are highly variable, warranting well-performing methods to serve as an accuracy base to improve the harmonization of C-peptide measurements in China. We developed an accurate isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) method for serum C-peptide measurement and explored its use in harmonization.Methods: After protein precipitation with ZnSO4 solution, C-peptide was extracted from serum samples by anion-exchange solid-phase extraction and quantified by ID-LC-MS/MS in positive ion mode. The precision and analytical recovery of the ID-LC-MS/MS method were assessed. Seventy-six serum samples were analyzed using the ID-LC-MS/MS method and six routine immunoassays. Ordinary linear regression (OLR) and Bland-Altman (BA) analyses were conducted to evaluate the relationship between the ID-LC-MS/MS method and routine immunoassays. Five serum pool samples assigned using the ID-LC-MS/MS method were used to recalibrate the routine assays. OLR and BA analyses were re-conducted after recalibration.
    Results: The within-run, between-run, and total precision for the ID-LC-MS/MS method at four concentrations were 1.0%-2.1%, 0.6%-1.2%, and 1.3%-2.2%, respectively. The analytical recoveries for the ID-LC-MS/MS method at three concentrations were 100.3%-100.7%, 100.4%-101.0%, and 99.6%-100.7%. The developed method and the immunoassays were strongly correlated, with all R2 >0.98. The comparability among the immunoassays was substantially improved after recalibration.
    Conclusions: The performance of the ID-LC-MS/MS method was carefully validated, and this method can be used to improve the harmonization of serum C-peptide measurements in China.
    Keywords:  Diabetes mellitus; Harmonization; Liquid chromatography-tandem mass spectrometry; Method comparison; Serum C-peptide
  9. Brief Bioinform. 2023 Mar 01. pii: bbad064. [Epub ahead of print]
      The use of stable isotope tracers and mass spectrometry (MS) is the gold standard method for the analysis of fatty acid (FA) metabolism. Yet, current state-of-the-art tools provide limited and difficult-to-interpret information about FA biosynthetic routes. Here we present FAMetA, an R package and a web-based application ( that uses 13C mass isotopologue profiles to estimate FA import, de novo lipogenesis, elongation and desaturation in a user-friendly platform. The FAMetA workflow covers the required functionalities needed for MS data analyses. To illustrate its utility, different in vitro and in vivo experimental settings are used in which FA metabolism is modified. Thanks to the comprehensive characterization of FA biosynthesis and the easy-to-interpret graphical representations compared to previous tools, FAMetA discloses unnoticed insights into how cells reprogram their FA metabolism and, when combined with FASN, SCD1 and FADS2 inhibitors, it enables the identification of new FAs by the metabolic reconstruction of their synthesis route.
    Keywords:  fatty acids; inhibitors; lipid metabolism; mass spectrometry; stable isotopes
  10. J Pharm Biomed Anal. 2023 Feb 25. pii: S0731-7085(23)00085-7. [Epub ahead of print]228 115316
      Steroidogenesis inhibitors such as metyrapone (MTP) and osilodrostat (ODT) have a key role in the medical treatment of endogenous Cushing's Syndrome (ECS). Both drugs are characterized by a high inter-individual variability of response and require a dose-titration period to achieve optimal control of cortisol excess. However, PK/PD data remain scarce for both molecules and a pharmacokinetically guided approach could help reaching eucortisolism more rapidly. We aimed to develop and validate a liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the simultaneous quantification of ODT and MTP in human plasma. After addition of isotopically labeled internal standard (IS), plasma pretreatment consisted in protein precipitation with acetonitrile including 1% formic acid (v/v). Chromatographic separation was performed on Kinetex® HILIC (4.6 × 50 mm; 2.6 µm) analytical column with an isocratic elution during the 2.0-min run time. The method was linear from 0.5 to 250 ng/mL for ODT and from 2.5 to 1250 ng/mL for MTP. Intra- and inter-assay precisions were < 7.2%, with an accuracy ranging from 95.9% to 114.9%. The IS-normalized matrix effect ranged from 106.0% to 123.0% (ODT) and from 107.0% to 123.0% (MTP) and the range of the IS-normalized extraction recovery was 84.0-101.0% for ODT and 87.0-101.0% for MTP. The LC-MS/MS method was successfully applied in patients' plasma samples (n = 36), trough concentration of ODT and MTP ranged from 2.7 ng/mL to 8.2 ng/mL and from 10.8 ng/mL to 27.8 ng/mL, respectively. Incurred sample reanalysis exhibits less than 14% difference between the first and the second analysis for both drugs. This accurate and precise method, meeting all validation criteria, can therefore be used for plasma drug monitoring of ODT and MTP within the dose-titration period.
    Keywords:  Cushing’s syndrome; LC-MS/MS; Metyrapone; Osilodrostat; Pharmacokinetics; Therapeutic drug monitoring
  11. Anal Chem. 2023 Feb 27.
      Free radical-mediated lipid peroxidation (LPO) induces the formation of numerous lipid radicals, which contribute to the development of several oxidative diseases. To understand the mechanism of LPO in biological systems and the significance of these radicals, identifying the structures of individual lipid radicals is imperative. In this study, we developed an analytical method based on liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) and a profluorescent nitroxide probe, N-(1-oxyl-2,2,6-trimethyl-6-pentylpiperidin-4-yl)-3-(5,5-difluoro-1,3-dimethyl-3H,5H-5l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-7-yl)propanamide (BDP-Pen), for the detailed structural analysis of lipid radicals. The MS/MS spectra of BDP-Pen-lipid radical adducts showed product ions and thus allow the prediction of the lipid radical structures and individual detection of isomeric adducts. Using the developed technology, we separately detected the isomers of arachidonic acid (AA)-derived radicals generated in AA-treated HT1080 cells. This analytical system is a powerful tool for elucidating the mechanism of LPO in biological systems.
  12. J Pharm Biomed Anal. 2023 Feb 27. pii: S0731-7085(23)00086-9. [Epub ahead of print]228 115317
      As an effective treatment for acute gouty arthritis and cardiovascular disease, colchicine is also a toxic alkaloid and may cause poisoning or even death in overdose. The study of colchicine elimination and the diagnosis of poisoning etiology need the rapid and accurate quantitative analysis method in biological matrix. An analytical method was developed for colchicine in plasma and urine by in-syringe dispersive solid phase extraction (DSPE) followed by liquid chromatography-triple quadrupole mass spectrometry (LC-MS/MS). Sample extraction and protein precipitation were proceeded with acetonitrile. The extract was cleaned by in-syringe DSPE. An XBridge™ BEH C18 column(100 mm × 2.1 mm, 2.5 µm)was used to separate colchicine by gradient elution with mobile phase of 0.01% (v/v) ammonia-methanol. The amount and filling sequence of magnesium sulfate (MgSO4) and primary secondary amine (PSA) suitable for in-syringe DSPE were studied. Scopolamine was screened as the quantitative internal standard (IS) for colchicine analysis according to the consistency of recovery rate, chromatographic retention time and matrix effects. The limits of detection for colchicine in plasma and urine were both 0.06 ng mL-1 and the limits of quantitation were both 0.2 ng mL-1. The linear range was 0.04 - 20 ng mL-1 (Equivalent to 0.2-100 ng mL-1 in plasma or urine) with a correlation coefficient r > 0.999. By IS calibration, the average recoveries at three spiking levels in plasma and urine were 95.3-102.68% and 93.9-94.8% with the relative standard deviations (RSDs) of 2.9-5.7% and 2.3-3.4%, respectively. The matrix effects, stability, dilution effects and carryover for determination of colchicine in plasma and urine were also evaluated. The elimination of colchicine within 72-384 h post-ingestion was studied for a poisoning patient with the doses of 1 mg d-1 for 39 days and then 3 mg d-1 for 15 days).
    Keywords:  Colchicine; Drug elimination; In-syringe dispersive solid phase extraction; Intoxication; Liquid chromatography; Triple quadrupole mass spectrometry
  13. bioRxiv. 2023 Feb 22. pii: 2023.02.22.529564. [Epub ahead of print]
      Nuclear Magnetic Resonance (NMR) spectroscopy is widely used to analyze metabolites in biological samples, but the analysis can be cumbersome and inaccurate. Here, we present a powerful automated tool, SPA-STOCSY (Spatial Clustering Algorithm - Statistical Total Correlation Spectroscopy), which overcomes the challenges by identifying metabolites in each sample with high accuracy. As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset, first investigating the covariance pattern and then calculating the optimal threshold with which to cluster data points belonging to the same structural unit, i.e. metabolite. The generated clusters are then automatically linked to a compound library to identify candidates. To assess SPA-STOCSY’s efficiency and accuracy, we applied it to synthesized and real NMR data obtained from Drosophila melanogaster brains and human embryonic stem cells. In the synthesized spectra, SPA outperforms Statistical Recoupling of Variables, an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the real spectra, SPA-STOCSY performs comparably to operator-based Chenomx analysis but avoids operator bias and performs the analyses in less than seven minutes of total computation time. Overall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. As such, it might accelerate the utilization of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making.
  14. Anal Methods. 2023 Feb 28.
      Determining and quantifying novel impurities and degraded impurities of a drug product is always a continuous challenge to enhancing the drug quality for patients' safety. Herein, our work deals with (i) developing a rapid, accurate, and reliable high-performance liquid chromatographic validation method to quantify the bictegravir drug (integrase inhibitors of antiretroviral drugs) and its novel related impurities at low levels, and (ii) the liquid chromatography-mass spectrometry (LC-MS) method to identify degraded impurities. Separation of bictegravir acid (impurity-I) and methyl bictegravir (impurity-II) impurities which are identified by LC-MS in the bictegravir drug was executed by developing a method and the same method performance evaluated by using full factorial design. This developed analytical technique gave a well-separated peak of bictegravir and related analytes such as bictegravir acid (impurity-I) and methyl bictegravir (impurity-II), adequate with the peak properties as per USP guidelines. The method's sensitivity and linearity are demonstrated by its detection and quantification limits at low levels with a correlation coefficient of 0.998. The method's repeatability, specificity, and accuracy suggest that this developed technique is a reliable determination strategy for the bictegravir drug substance and its related impurities (impurity-I and impurity-II) in a simple, feasible, and affordable way.
  15. J Anal Toxicol. 2023 Mar 03. pii: bkad017. [Epub ahead of print]
      Anticoagulant rodenticides (ARs) are commonly utilized for controlling rodent populations, however non-target companion and wildlife animals are also exposed. A method was developed for quantitation of seven ARs (chlorophacinone, coumachlor, bromadiolone, brodifacoum, difethialone, diphacinone, and warfarin) and dicoumarol (a naturally occurring anticoagulant) in animal serum. Analytes were extracted with 10% (v/v) acetone in methanol and analyzed by reverse phase high-pressure liquid chromatograph-tandem mass spectrometry (HPLC-MS/MS) using electrospray ionization (negative mode) combined with multiple reaction monitoring (MRM). In-house method validation in the originating laboratory using non-blinded samples revealed method limits of quantitation at 2.5 ng/mL for all analytes. Inter-assay accuracy ranged 99-104% and relative standard deviation ranged 3.5-20.5%. Method performance was then verified in the originating laboratory during an exercise organized by an independent party using blinded samples. The method was successfully transferred to two naïve laboratories and further evaluated for reproducibility among three laboratories by means of Horwitz ratio (HorRat(R)) values. Such extensive validation provides a high degree of confidence that the method is rugged, robust, and will perform as expected if used by others in the future.
    Keywords:  HorRat; LC-MS/MS; anticoagulant; blinded method test; hydroxycoumarins; indanediones; rodenticides
  16. J Chromatogr A. 2023 Feb 16. pii: S0021-9673(23)00102-4. [Epub ahead of print]1693 463874
      The current study describes the development of a 2D-LC-MS-based strategy for assessing main peak purity in the analysis of pharmaceutical peptides. The focus is on 2D-LC using reversed-phase (RP) separations in both dimensions, and particularly peptide isomer selectivity, since compounds with the same mass to charge ratio are not readily differentiated by mass spectrometry and therefore must be separated chromatographically. Initially, 30 column / mobile phase combinations were evaluated for both general separation performance (i.e., selectivity and peak shape) and isomer selectivity using forcibly degraded peptide samples and mixtures of synthetic diastereomers. A ranking of more than 300 UV and MS chromatograms suggests that when developing a new method, screening a set of four columns and four volatile mobile phases with differing characteristics should be adequate to both cover the selectivity space, and yield good separation performance. When 2D-LC-MS is to be used to evaluate peak purity for a new method, our results show that a second-dimension separation comprising a C8/C18 column possessing no ionic functionality, and an acetic acid / ammonium acetate mobile phase buffered at pH 5, provides good selectivity at 25 °C for peptide isomers with a MW <10 kDa. Retention data for 29 diverse peptides (1 < MW < 14 kDa, 3.7 < pI < 12.5) measured in this study using a variety of column and mobile phase conditions (i.e., 30 in total) are consistent with the classification of these various chromatographic conditions using the previously reported Peptide RPC Column Characterisation Protocol. For the investigated peptides trifluoroacetic acid was found to reduce selectivity differences between columns of diverse properties, probably due to its potential to form ion-pairs with peptides. Trifluoroacetic acid often improves peak shape for very large peptides (i.e. MW > 10 kDa). In the current dataset which also contain smaller peptides it received the highest ranking for 40% of the column and mobile phase combinations due to better selectivity and/or peak shape. The reported work here constitutes part one of a series of two papers. The second paper focuses on the use of retention modelling for rapid and accurate selection of the shallow gradients (i.e., << 1% ACN/min) required to obtain sufficient peptide isomer retention and separation in the second dimension. The overall results presented in this series of papers provides the guidance needed to develop a 2D-LC-MS method from start to finish for the analysis of main peak purity of therapeutic peptides.
    Keywords:  2D-RPC-MS; Mobile phase; Peak purity; Peptides; Stationary phase
  17. Se Pu. 2023 Mar;41(3): 250-256
      At present, new prohibited substances are becoming more common illegal additions in cosmetics. Clobetasol acetate is a new glucocorticoid, which is not covered in the current national standards and is a homologue of clobetasol propionate. A method was established for the determination of clobetasol acetate as a new glucocorticoid (GC) in cosmetics by ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Five common cosmetic matrices were suitable for this new method: creams, gels, clay masks, masks and lotions. Four pretreatment methods were compared: direct extraction by acetonitrile, PRiME pass-through column purification, solid-phase extraction (SPE) purification, and QuEChERS purification. Further, the effects of different extraction efficiencies of the target compound, such as extraction solvents and extraction time, were investigated. The MS parameters, such as ion mode, cone voltage and collision energy of ion pairs of the target compound, were optimized. The chromatographic separation conditions and response intensities of the target compound in different mobile phases were compared. Based on the experimental results, the optimal extraction method was determined to be direct extraction, wherein the samples were vortex dispersed with acetonitrile, ultrasonic extraction over 30 min and filtered by a 0.22 μm organic millipore filter, and then the samples were detected by UPLC-MS/MS. The concentrated extracts were separated on a Waters CORTECS C18 column (150 mm×2.1 mm, 2.7 μm), where the water and acetonitrile were used as the mobile phases for gradient elution. The target compound was detected with the multiple reaction monitoring (MRM) mode under electrospray ionization and positive ion scanning (ESI+). Quantitative analysis was performed by matrix matching standard curve. Under the optimum conditions, the target compound had good linear fitting in the range of 0.9-37 μg/L. The linear correlation coefficient (R2) was greater than 0.99, the limit of quantification (LOQ) of the method was 0.09 μg/g and the limit of detection (LOD) was 0.03 μg/g for these five different cosmetic matrices. The recovery test was conducted under three spiked levels: 1, 2 and 10 times of LOQ. The recoveries of the tested substance were between 83.2% and 103.2% in these five cosmetic matrices, and the relative standard deviations (RSDs, n=6) were between 1.4% and 5.6%. This method was used to screen cosmetic samples of different matrix types, and a total of five positive samples were found, in which the content range of clobetasol acetate was from 1.1 to 48.1 μg/g. In conclusion, the method is simple, sensitive and reliable, and is suitable for high-throughput qualitative and quantitative screening, and the analysis of cosmetics with different matrix types. Moreover, the method provides crucial technical support and a theoretical basis for the establishment of feasible detection standards for clobetasol acetate in China, as well as for the control of the compound in cosmetics. This method has important practical significance to implement management measures of illegal additions in cosmetics.
    Keywords:  clobetasol acetate; cosmetics; glucocorticoids; ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  18. Biomed Chromatogr. 2023 Feb 27. e5612
      The mixture of Hyoscine N-butyl bromide (HBB) and Ketoprofen (KTP) is commonly used for the handling of abdominal spasms and pain reliever. There are two challenges that restrict the simultaneous assessment of HBB and KTP in biological fluids and pharmaceuticals, the first issue is the difficulty of elution of HBB and the second one is the presence of KTP as a racemic mixture in all pharmaceutical formulations that obscure the appearance of it as a single peak. An ultra-sensitive and highly efficient liquid chromatography-mass/mass spectrometric (LC-MS/MS) method is designed and validated for the first concurrent assessment of HBB and KTP in spiked human serum and urine, and pharmaceutical formulations. The estimated linearity ranges for HBB and KTP were respectively, 0.5 - 500 ng/mL and 0.05-500 ng/mL, with excellent correlation coefficients. Validation results showed that the value of relative standard deviations (RSDs) were less than 2 % for HBB and KTP. The mean extraction recoveries for HBB and KTP were respectively, 91.04 and 97.83 % in spasmofen® ampoules; 95.89 and 97.00 % in spiked serum; 97.31 and 95.63 in spiked urine. The presented innovative chromatographic approach was utilized for the measurement of trace amounts of coexisting pharmaceuticals in pharmacokinetics studies and routine therapeutic medication monitoring.
    Keywords:  Hyoscine N-butyl bromide; Ketoprofen; LC-MS/MS; biological fluids; pharmaceuticals
  19. J Pharmacol Toxicol Methods. 2023 Feb 28. pii: S1056-8719(23)00005-9. [Epub ahead of print] 107254
      BACKGROUND: A novel, sensitive and specific LC-MS/MS technique was developed and validated for the quantification of fostemsavir in human plasma and its pharmacokinetic application in rabbits.METHODS: Chromatographic separation of the fostemsavir and fosamprenavir (internal standard) were achieved on Zorbax C18 (50 mm × 2 mm × 5 μm) column with 0.80 mL/min flow rate and coupled with API6000 triple quadrupole MS in multi reaction monitoring mode by applying mass transitions m/z 584.16/105.03 for fostemsavir and m/z 586.19/57.07 for the internal standard.
    RESULTS: The calibration curve exhibited linearity in concentration range of 58.5-2340.0 ng/mL for fostemsavir. The LLOQ was 58.5 ng/mL. The validated LC-MS/MS process was effectively applied for the analysis of plasma in healthy rabbits for determinations of Fostemsavir. From the pharmacokinetic data, the mean of Cmax and Tmax were 198.19 ± 5.85 ng/mL and 2.42 ± 0.13, respectively. Plasma conc. Reduced with t1/2 of 7.02 ± 0.14. AUC0→Last value obtained was 2374.87 ± 29.75 ng. h/ml, respectively.
    CONCLUSION: In summary, the developed method has been successfully validated and pharmacokinetic parameters were demonstrated after oral administration of Fostemsavir to healthy rabbits.
    Keywords:  Fostemsavir; HIV/AIDS; LC-MS/MS; Pharmacokinetics; Rabbits; Validation
  20. Se Pu. 2023 Mar;41(3): 233-240
      Quaternary ammonium compounds (QACs) are a class of cationic surfactants that can be used as the main active ingredient of disinfectants. The increased use of QACs is concerning as exposure from inhalation or ingestion to these compounds that has been associated with adverse effects on the reproductive and respiratory systems. Humans are exposed to QACs primarily by food consumption and inhalation of air. QAC residues pose significant threats to public health. Given the importance of assessing potential residue levels for QACs in food, therefore, a method was developed for the simultaneous detection of six common QACs and one emerging QAC (Ephemora) in frozen food by ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) coupled with the modified QuEChERS method. The main factors governing the response, recovery, and sensitivity of the method, including extraction solvents, types and dosages of adsorbents, apparatus conditions, and mobile phases, were optimized in the course of sample pretreatment and instrument analysis. QAC residues in frozen food were extracted using 20 mL methanol-water (90∶10, containing 0.5% formic acid) for 20 min by the vortex shock method. The mixture was ultrasonicated for 10 min and centrifuged at 10000 r/min for 10 min. A 1-mL aliquot of the supernatant was transferred to a new tube and purified using 100 mg of PSA adsorbents. After mixing and centrifugation at 10000 r/min for 5 min, the purified solution was analyzed. Target analytes were separated on an ACQUITY UPLC BEH C8 chromatographic column (50 mm×2.1 mm, 1.7 μm) at a column temperature of 40 ℃ and a flow rate of 0.3 mL/min. The injection volume was 1 μL. Gradient elution was performed using methanol and 5 mmol/L ammonium acetate solution as the mobile phases. Multiple reaction monitoring (MRM) was conducted in the positive electrospray ionization (ESI+) mode. The matrix-matched external standard method was used to quantify seven QACs. The optimized chromatography-based method completely separated the seven analytes. Good linear relationships were obtained for the seven QACs in the range of 0.1-100.0 ng/mL. The correlation coefficient (r2) ranged from 0.9971 to 0.9983. The limits of detection and limits of quantification ranged from 0.5 to 1.0 μg/kg and 1.5 to 3.0 μg/kg, respectively. Accuracy and precision were determined by spiking salmon and chicken samples with 3.0, 10.0, and 100.0 μg/kg of analytes, in compliance with the current legislation, with six replicates per determination. The average recoveries of the seven QACs ranged from 65.4% to 101%. The relative standard deviations (RSDs) were between 0.64% and 16.8%. Matrix effects of the analytes were between -27.5% and 33.4% in salmon and chicken samples after purifying using PSA. The developed method was applied to the determination of seven QACs in rural samples. QACs were detected in only one sample; the level did not exceed European Food Safety Authority specified residue limit standards. The detection method has high sensitivity, good selectivity and stability, and the results are accurate and reliable. It is suitable for the simultaneous rapid determination of seven QAC residues in frozen food. The results provide valuable information for future risk assessment studies targeting this class of compounds.
    Keywords:  QuEChERS; frozen food; quaternary ammonium compounds (QACs); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  21. Bioinformatics. 2023 Mar 02. pii: btad078. [Epub ahead of print]
      MOTIVATION: Annotation of the mass signals is still the biggest bottleneck for the untargeted mass spectrometry analysis of complex mixtures. Molecular networks are being increasingly adopted by the mass spectrometry community as a tool to annotate large scale experiments. We have previously shown that the process of propagating annotations from spectral library matches on molecular networks can be automated using Network Annotation Propagation (NAP). One of the limitations of NAP is that the information for the spectral matches is only propagated locally, to the first neighbor of a spectral match. Here we show that annotation propagation can be expanded to nodes not directly connected to spectral matches using random walks on graphs, introducing the ChemWalker python library.RESULTS: Similarly to NAP, ChemWalker relies on combinatorial in silico fragmentation results, performed by MetFrag, searching biologically relevant databases. Departing from the combination of a spectral network and the structural similarity among candidate structures, we have used MetFusion Scoring function to create a weight function, producing a weighted graph. This graph was subsequently used by the random walk to calculate the probability of 'walking' through a set of candidates, departing from seed nodes (represented by spectral library matches). This approach allowed the information propagation to nodes not directly connected to the spectral library match. Compared to NAP, ChemWalker has a series of improvements, on running time, scalability and maintainability and is available as a stand alone python package.
    AVAILABILITY: ChemWalker is freely available at
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  22. Se Pu. 2023 Mar;41(3): 241-249
      The widespread and frequent use of antibiotics to treat diseases or encourage animal growth has resulted in their persistence and accumulation in water, soil, and sediments. As a typical emerging pollutant in the environment, antibiotics have become an important research focus in recent years. Antibiotics are commonly found at trace levels in water environments. Unfortunately, the determination of various types of antibiotics, all of which exhibit different physicochemical properties, remains a challenging endeavor. Thus, developing pretreatment and analytical techniques to achieve the rapid, sensitive, and accurate analysis of these emerging contaminants in various water samples is an essential undertaking.In this paper, a solid phase extraction-high performance liquid chromatography-tandem mass spectrometry (SPE-HPLC-MS/MS) method for the simultaneous determination of 22 antibiotics including 4 penicillins, 12 quinolones and 6 macrolides in environmental water samples was developed. Based on the characteristics of the screened antibiotics and sample matrix, the pretreatment method was optimized, focusing on the SPE column, pH of the water sample, and amount of ethylene diamine tetra-acetic acid disodium (Na2EDTA) added to the water sample. Prior to extraction, a 200 mL water sample was added with 0.5 g of Na2EDTA and pH-adjusted to 3 using sulfuric acid or sodium hydroxide solution. Water sample enrichment and purification were achieved using an HLB column. HPLC separation was carried out on a C18 column (100 mm×2.1 mm, 3.5 μm) via gradient elution with a mobile phase composed of acetonitrile and 0.15% (v/v) formic acid aqueous solution. Qualitative and quantitative analyses were performed on a triple quadrupole mass spectrometer in multiple reaction monitoring mode using an electrospray ionization source. The results showed correlation coefficients greater than 0.995, indicating good linear relationships. The method detection limits (MDLs) and limits of quantification (LOQs) were in the ranges of 2.3-10.7 ng/L and 9.2-42.8 ng/L, respectively. The recoveries of target compounds in surface water at three spiked levels ranged from 61.2% to 157%, with relative standard deviations (RSDs) of 1.0%-21.9%. The recoveries of target compounds in wastewater at three spiked levels were 50.1%-129%, with RSDs of 1.2%-16.9%. The method was successfully applied to the simultaneous determination of antibiotics in reservoir water, surface water, sewage treatment plant outfall, and livestock wastewater. Most of the antibiotics were detected in watershed and livestock wastewater. Lincomycin was detected in 10 surface water samples, with a detection frequency of 90%, and ofloxacin showed the highest contents (127 ng/L) in livestock wastewater. Therefore, the present method exhibits excellent performance in terms of MDLs and recoveries compared with previously reported methods. The developed method presents the advantages of small water sample volumes, wide applicability, and fast analysis times; thus, it can be considered a rapid, efficient, and sensitive analytical method with excellent potential for monitoring emergency environmental pollution. The method could also provide a reliable reference for formulating antibiotic residue standards. The results provide strong support for and an improved understanding of the environmental occurrence, treatment, and control of emerging pollutants.
    Keywords:  antibiotics; environmental water samples; high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS); liquid; solid phase extraction (SPE)
  23. Trends Biochem Sci. 2023 Feb 28. pii: S0968-0004(23)00034-8. [Epub ahead of print]
      Isotope-assisted metabolic flux analysis (iMFA) is a powerful method to mathematically determine the metabolic fluxome from experimental isotope labeling data and a metabolic network model. While iMFA was originally developed for industrial biotechnological applications, it is increasingly used to analyze eukaryotic cell metabolism in physiological and pathological states. In this review, we explain how iMFA estimates the intracellular fluxome, including data and network model (inputs), the optimization-based data fitting (process), and the flux map (output). We then describe how iMFA enables analysis of metabolic complexities and discovery of metabolic pathways. Our goal is to expand the use of iMFA in metabolism research, which is essential to maximizing the impact of metabolic experiments and continuing to advance iMFA and biocomputational techniques.
    Keywords:  fluxomics; mass spectrometry; metabolic modeling isotope labeling
  24. J Proteome Res. 2023 Mar 03.
      We have used household consumables to facilitate electrochemical etching of stainless-steel hypodermic tubing to produce tapered-tip emitters suitable for electrospray ionization for use in mass spectrometry. The process involves the use of 1% oxalic acid and a 5 W USB power adapter, commonly known as a phone charger. Further, our method avoids the otherwise commonly used strong acids that entail chemical hazards: concentrated HNO3 for etching stainless steel, or concentrated HF for etching fused silica. Hence, we here provide a convenient and self-inhibiting procedure with minimal chemical hazards to manufacture tapered-tip stainless-steel emitters. We show its performance in metabolomic analysis with CE-MS of a tissue homogenate where the metabolites acetylcarnitine, arginine, carnitine, creatine, homocarnosine, and valerylcarnitine were identified, all with basepeak separated electropherograms, within <6 min of separation. The mass spectrometry data are freely available through the MetaboLight public data repository via access number MTBLS7230.
    Keywords:  CE−MS; electrochemical etching; electrospray ionization; stainless-steel emitter; tapered tip