bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒04‒09
23 papers selected by
Sofia Costa

  1. Se Pu. 2023 Apr;41(4): 366-375
      Monoaromatic hydrocarbons (MAHs) such as benzene, toluene, and xylene are important anthropogenic pollutants in the urban atmosphere. The detection of urinary MAH metabolites are included in human biomonitoring programs in several countries, including Canada, the United States, Italy, and Germany, because their evaluation is vital to monitor the exposure of humans to MAHs. To this end, herein, a method was developed for the determination of seven MAH metabolites through ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). An aliquot of 0.5 mL urine was fortified with an isotopic labeled internal standard solution before being hydrolyzed by 40 μL of 6 mol/L HCl solution, followed by extraction using a 96-well EVOLUTE®EXPRESS ABN solid-phase extraction plate. The samples were washed with 1.0 mL of methanol-water (10∶90, v/v) and eluted with 1.0 mL methanol. The eluate was diluted four times with water prior to use in instrumental analysis. Chromatographic separation was achieved using an ACQUITY UPLC HSS T3 column (100 mm×2.1 mm, 1.8 μm), with gradient elution using 0.1% formic acid as mobile phase A and methanol as mobile phase B. The detection of seven analytes was performed using a triple-quadrupole mass spectrometer equipped with a negative electrospray ionization source in the multiple reaction monitoring mode. The linear ranges of the seven analytes varied from 0.1-20 μg/L to 2.5-500 mg/L, with correlation coefficients greater than 0.995. The method detection limits were 1.5, 0.02, 0.1, 900, 0.6, and 4 μg/L for trans,trans-muconic acid (MU), S-phenylmercapturic acid (PMA), S-benzylmercapturic acid (BMA), hippuric acid (HA), 2-methyl hippuric acid (2MHA), and 3-methyl hippuric acid (3MHA)+4-methyl hippuric acid (4MHA), respectively. The limits of quantification were 5, 0.05, 0.4, 3000, 2, and 12 μg/L for MU, PMA, BMA, HA, 2MHA, and 3MHA+4MHA, respectively. The method was verified by spiking urine samples at three different concentration levels, with recovery rates ranging from 84% to 123%. The intra- and inter-day precisions were 1.8%-8.6% and 1.9%-21.4%, respectively. The extraction efficiencies were 68%-99%, and the matrix effects ranged from -11% to -87%. The urine samples obtained from the German external quality assessment scheme (round 65) were used to assess the accuracy of this method. Both high and low concentrations of MU, PMA, HA, and methyl hippuric acid were within the tolerance range. All analytes in the urine samples were found to be stable for up to seven days at room temperature (20 ℃, absence of light), with less than 15% change in concentration. Analytes in urine samples were found to be stable for at least 42 d at 4 ℃ and -20 ℃, or for six freeze-thaw cycles and up to 72 h in an autosampler (8 ℃). The method was applied to the analysis of 16 non-smokers' and 16 smokers' urine samples. The detection rates of MU, BMA, HA, and 2MHA were 100% in both non-smokers' and smokers' urine samples. PMA was detected in 75% non-smokers' and 100% smokers' urine samples. 3MHA+4MHA was detected in 81% non-smokers' urine and in all smokers' urine samples. Statistical differences were found for MU, PMA, 2MHA, and 3MHA+4MHA between the two groups (p<0.001). The established method has good robustness and can provide reliable results. The experiments were carried out in a high-throughput manner with large sample sizes, owing to the small sample volume, and allowed the successful detection of the seven MAH metabolites in human urine.
    Keywords:  biomonitoring; monoaromatic hydrocarbon metabolites; ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); urine
  2. Magn Reson Chem. 2023 Apr 02.
      Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize a few hundred metabolites at best. The uncertainty in metabolite identification commonly encountered in untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple analytical techniques) approach can improve upon the number of metabolites reliably detected and correctly assigned. This can be further improved by applying synergistic sample preparation along with the use of combinatorial or sequential non-destructive and destructive techniques. Similarly, peak detection and metabolite identification strategies that employ multiple probabilistic approaches have led to better annotation decisions. Applying these techniques also addresses the issues of reproducibility found in single platform methods. Nevertheless, the analysis of large data sets from disparate analytical techniques presents unique challenges. While the general data processing workflow is similar across multiple platforms, many software packages are only fully capable of processing data types from a single analytical instrument. Traditional statistical methods such as principal component analysis were not designed to handle multiple, distinct data sets. Instead, multivariate analysis requires multiblock or other model types for understanding the contribution from multiple instruments. This review summarizes the advantages, limitations, and recent achievements of a multiplatform approach to untargeted metabolomics.
    Keywords:  mass spectrometry; metabolite assignment; metabolome coverage; metabolomics; multiplatform; nuclear magnetic resonance
  3. Se Pu. 2023 Apr;41(4): 312-322
      A rapid and sensitive method based on ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed for the simultaneous determination of 12 typical personal care products (PCPs) in human urine. These PCPs included five paraben preservatives (PBs), five benzophenone UV absorbers (BPs), and two antibacterial agents. Accordingly, 1 mL of the urine sample was mixed with 500 μL of β-glucuronidase-ammonium acetate buffer solution (enzymatic activities are 500 units/mL) and 75 μL of a mixed internal standard working solution (internal standard contents are 7.5 ng), followed by enzymatic hydrolysis overnight (≥16 h) at 37 ℃ in a water bath. The 12 targeted analytes were enriched and cleaned up using an Oasis HLB solid phase extraction column. Separation was performed on an Acquity BEH C18 column (100 mm×2.1 mm, 1.7 μm) using an acetonitrile-water system as the mobile phase, in negative electrospray ionization (ESI-) multiple reaction monitoring (MRM) mode, for target detection and stable isotope internal standard quantification. The optimal MS conditions were established by optimizing the instrument parameters and comparing two analytical columns (Acquity BEH C18 and Acquity UPLC HSS T3) as well as different types of mobile phases (methanol or acetonitrile as the organic phase) to achieve better chromatographic separation. In order to obtain higher enzymatic and extraction efficiency, different enzymatic conditions, solid phase extraction columns, and elution conditions were investigated. The final results showed that methyl parabens (MeP), benzophenone-3 (BP-3), and triclosan (TCS) showed good linearities in the ranges of 4.00-800, 4.00-800 and 5.00-200 μg/L, respectively, the other targeted compounds showed good linearities in the ranges of 1.00-200 μg/L. The correlation coefficients were all greater than 0.999. The method detection limits (MDLs) were in the range of 0.06-1.09 μg/L, and the method quantification limits (MQLs) ranged from 0.08 to 3.63 μg/L. At three spiked levels, the average recoveries of the 12 targeted analytes ranged from 89.5% to 111.8%. The intra-day and inter-day precisions were 3.7%-8.9% and 2.0%-10.6%, respectively. The results of the matrix effect assessment showed that MeP, ethyl paraben (EtP), and benzophenone-2 (BP-2) exhibited strong matrix effects (26.7%-103.8%); propyl paraben (PrP) exhibited moderate matrix effects (79.2%-112.0%); and the other eight target analytes exhibited weak matrix effects (83.3%-113.8%). The matrix effects of the 12 targeted analytes after correction using the stable isotopic internal standard method ranged from 91.9% to 110.1%. The developed method was successfully applied to the determination of the 12 PCPs in 127 urine samples. Ten typical PCPs were detected, with the overall detection rates ranging from 1.7% to 99.7%, except for benzyl paraben (BzP) and benzophenone-8 (BP-8). The results revealed that the population in this area was widely exposed to PCPs, especially MeP, EtP and PrP; the detection rates and concentrations of these PCPs were found to be very high. Our analytical method is simple and sensitive, and it is expected to be an effective tool for biomonitoring PCPs in human urine samples as part of environmental health studies.
    Keywords:  biomonitoring; personal care products (PCPs); solid phase extraction (SPE); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); urine
  4. Clin Chem Lab Med. 2023 Apr 04.
      OBJECTIVES: To develop an isotope dilution-liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based candidate reference measurement procedure (RMP) for levetiracetam quantification in human serum and plasma.METHODS: Quantitative nuclear magnetic resonance spectroscopy (qNMR) was used to characterize the RMP material to ensure traceability to SI units. To quantify levetiracetam, an LC-MS/MS method was optimized using a C8 column for chromatographic separation following protein-precipitation-based sample preparation. Spiked matrix samples of serum and plasma were used to test selectivity and specificity. Matrix effects were determined by performing a post-column infusion experiment and comparing standard line slopes. Precision and accuracy were evaluated over 5 days. Measurement uncertainty was evaluated according to the Guide to the Expression of Uncertainty in Measurement (GUM).
    RESULTS: The RMP was proven to be highly selective and specific with no evidence of a matrix effect, allowing for quantification of levetiracetam within the range of 1.53-90.0 μg/mL. Intermediate precision was <2.2% and repeatability was 1.1-1.7% across all concentrations. The relative mean bias ranged from -2.5% to -0.3% across all levels and matrices within the measuring range. Diluted samples were found with a mean bias ranging from -0.1 to 2.9%. The predefined acceptance criterion for measurement uncertainty was met and determined for individual measurements independently of the concentration level and sample type to be ≤4.0% (k=2).
    CONCLUSIONS: We present a novel LC-MS/MS)-based candidate RMP for levetiracetam in human serum and plasma. Its expanded measurement uncertainty of ≤4.0% meets the clinical needs in levetiracetam monitoring. Utilizing qNMR to characterize levetiracetam reference materials allowed metrological traceability to SI units.
    Keywords:  SI units; isotope dilution-liquid chromatography-tandem mass spectrometry; levetiracetam; qNMR; reference measurement procedure; traceability
  5. Clin Chem Lab Med. 2023 Apr 04.
      OBJECTIVES: To develop a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify 41 different purine and pyrimidine (PuPy) metabolites in human urine to allow detection of most known disorders in this metabolic pathway and to determine reference intervals.METHODS: Urine samples were diluted with an aqueous buffer to minimize ion suppression. For detection and quantification, liquid chromatography was combined with electrospray ionization, tandem mass spectrometry and multiple reaction monitoring. Transitions and instrument settings were established to quantify 41 analytes and nine stable-isotope-labeled internal standards (IS).
    RESULTS: The established method is precise (intra-day CV: 1.4-6.3%; inter-day CV: 1.3-15.2%), accurate (95.2% external quality control results within ±2 SD and 99.0% within ±3 SD; analyte recoveries: 61-121%), sensitive and has a broad dynamic range to quantify normal and pathological metabolite concentrations within one run. All analytes except aminoimidazole ribonucleoside (AIr) are stable before, during and after sample preparation. Moreover, analytes are not affected by five cycles of freeze-thawing (variation: -5.6 to 7.4%), are stable in thymol (variation: -8.4 to 12.9%) and the lithogenic metabolites also in HCl conserved urine. Age-dependent reference intervals from 3,368 urine samples were determined and used to diagnose 11 new patients within 7 years (total performed tests: 4,206).
    CONCLUSIONS: The presented method and reference intervals enable the quantification of 41 metabolites and the potential diagnosis of up to 25 disorders of PuPy metabolism.
    Keywords:  LC-MS/MS; diagnosis; purines; pyrimidines; reference intervals; stability
  6. Anal Chem. 2023 Apr 05.
      In untargeted metabolomics, multiple ions are often measured for each original metabolite, including isotopic forms and in-source modifications, such as adducts and fragments. Without prior knowledge of the chemical identity or formula, computational organization and interpretation of these ions is challenging, which is the deficit of previous software tools that perform the task using network algorithms. We propose here a generalized tree structure to annotate ions in relationships to the original compound and infer neutral mass. An algorithm is presented to convert mass distance networks to this tree structure with high fidelity. This method is useful for both regular untargeted metabolomics and stable isotope tracing experiments. It is implemented as a Python package (khipu) and provides a JSON format for easy data exchange and software interoperability. By generalized preannotation, khipu makes it feasible to connect metabolomics data with common data science tools and supports flexible experimental designs.
  7. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Mar 23. pii: S1570-0232(23)00088-0. [Epub ahead of print]1222 123678
      A selective and sensitive liquid chromatography-tandem mass spectrometry method was developed and validated for accurate determination of CHF6550 and its main metabolite in rat plasma and lung homogenate samples. All biological samples were prepared by simple protein precipitation method using deuterated internal standards. The analytes were separated on a HSS T3 analytical column with 3.2 min run time at flow rate of 0.5 mL/min. The detection was performed on a triple-quadrupole tandem mass spectrometer equipped with positive-ion electrospray ionization by selected-reaction monitoring of the transitions at m/z 735.3 → 98.0 for CHF6550 and m/z 638.3 → 319.2 and 638.3 → 376.2 for CHF6671. The calibration curves for plasma samples were linear between 50 and 50000 pg/mL for both analytes. The calibration curves for lung homogenate samples were linear within 0.1-100 ng/mL for CHF6550 and 0.3-300 ng/mL for CHF6671. The method was successfully applied to a 4-week toxicity study.
    Keywords:  CHF6550; CHF6671; LC-MS/MS; Rat Lung homogenate; Rat plasma
  8. Front Mol Biosci. 2023 ;10 1112521
      It is increasingly evident that a more detailed molecular structure analysis of isomeric lipids is critical to better understand their roles in biological processes. The occurrence of isomeric interference complicates conventional tandem mass spectrometry (MS/MS)-based determination, necessitating the development of more specialised methodologies to separate lipid isomers. The present review examines and discusses recent lipidomic studies based on ion mobility spectrometry combined with mass spectrometry (IMS-MS). Selected examples of the separation and elucidation of structural and stereoisomers of lipids are described based on their ion mobility behaviour. These include fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. Recent approaches for specific applications to improve isomeric lipid structural information using direct infusion, coupling imaging, or liquid chromatographic separation workflows prior to IMS-MS are also discussed, including: 1) strategies to improve ion mobility shifts; 2) advanced tandem MS methods based on activation of lipid ions with electrons or photons, or gas-phase ion-molecule reactions; and 3) the use of chemical derivatisation techniques for lipid characterisation.
    Keywords:  identification; ion mobility spectrometry (IMS); lipid isomers; lipidomics; mass spectrometry (MS); separation; stereoisomers; structural isomers
  9. Anal Chem. 2023 Apr 06.
      There is great demand for analytical methods capable of providing high-throughput and rapid screening, especially for anti-doping and clinical point-of-care applications. In this work, automated microfluidic open interface-mass spectrometry (MOI-MS) was used for coupling with high-throughput, automated solid-phase microextraction (SPME) to achieve this objective. The design of the MOI-MS interface provides a continuous and stable electrospray fluid flow to the MS without introducing any bubble, a feature that we exploit to introduce the concept of multi-segment injection for the determination of multiple samples in a single MS run. By eliminating the need to start a new MS run between sample assays, the developed approach provides significantly simplified protocols controlled by programmed software and increased reproducibility. Furthermore, the biocompatible SPME device, which utilizes coating consisting of hydrophilic-lipophilic balanced particles embedded in a polyacrylonitrile (PAN) binder, can be directly used for biological sample analysis, as the PAN acts as both a binder and a matrix-compatible barrier, thus enabling the enrichment of small molecules while eliminating interferences associated with the presence of interfering macromolecules. The above design was employed to develop a fast, quantitative method capable of analyzing drugs of abuse in saliva samples in as little as 75 s per sample. The findings indicate that the developed method provides good analytical performance, with limits of detection ranging between 0.05 and 5 ng/mL for analysis of 16 drugs of abuse, good calibration linear correlation coefficients (R2 ≥ 0.9957), accuracy between 81 and 120%, and excellent precision (RSD% < 13%). Finally, a proof-of-concept experiment was performed to demonstrate the method's suitability for real-time analysis in anti-doping applications.
  10. Anal Chim Acta. 2023 May 08. pii: S0003-2670(23)00349-5. [Epub ahead of print]1254 341128
      In this work, the collision cross section (CCS) value of 103 steroids (including unconjugated metabolites and phase II metabolites conjugated with sulfate and glucuronide groups) was determined by liquid chromatography coupled to traveling wave ion mobility spectrometry (LC-TWIMS). A time of flight (QTOF) mass analyzer was used to perform the analytes determination at high-resolution mass spectrometry. An electrospray ionization source (ESI) was used to generate [M+H]+, [M + NH4]+ and/or [M - H]- ions. High reproducibility was observed for the CCS determination in both urine and standard solutions, obtaining RSD lower than 0.3% and 0.5% in all cases respectively. CCS determination in matrix was in accordance with the CCS measured in standards solution showing deviations below 2%. In general, CCS values were directly correlated with the ion mass and allowed differentiating between glucuronides, sulfates and free steroids although differences among steroids of the same group were less significant. However, more specific information was obtained for phase II metabolites observing differences in the CCS value of isomeric pairs concerning the conjugation position or the α/β configuration, which could be useful in the structural elucidation of new steroid metabolites in the anti-doping field. Finally, the potential of IMS reducing interferences from the sample matrix was also tested for the analysis of a glucuronide metabolite of bolasterone (5β-androstan-7α,17α-dimethyl-3α,17β-diol-3-glucuronide) in urine samples.
    Keywords:  Anti-doping; Collision cross section; Ion mobility; Isomeric compounds; Urine analysis
  11. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Mar 11. pii: S1570-0232(23)00064-8. [Epub ahead of print]1221 123654
      The selective estrogen receptor modifier tamoxifen (TAM) is widely used for the treatment of women with estrogen receptor positive (ER+ ) breast cancer. Endoxifen (ENDX) is a potent, active metabolite of TAM and is important for TAM's clinical activity. While multiple papers have been published regarding TAM metabolism, few studies have examined or quantified the metabolism of ENDX. To quantify ENDX and its metabolites in patient plasma samples, we have developed and validated a rapid, sensitive, and specific liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the quantitative determination of the E- and Z-isomers of ENDX (0.5-500 ng/ml) and the ENDX metabolites norendoxifen (1-500 and 0.5-500 ng/ml E and Z, respectfully), ENDX catechol (3.075-307.5 and 1.92-192 ng/ml E and Z, respectfully), 4'-hydroxy ENDX (0.33-166.5 and 0.33-333.5 ng/ml E and Z, respectfully), ENDX methoxycatechol (0.3-300 and 0.2-200 ng/ml E and Z, respectfully), and ENDX glucuronide (2-200 and 3-300 ng/ml E and Z, respectfully) in human plasma. Chromatographic separation was accomplished on a HSS T3 precolumn attached to an Poroshell 120 EC-C18 analytical column using 0.1 % formic acid/water and 0.1 % formic acid/methanol as eluents followed by MS/MS detection. The analytical run time was 6.5 min. Standard curves were linear (R2 ≥ 0.98) over the concentration ranges. The intra- and inter-day precision and accuracy, determined at high-, middle-, and low-quality control concentrations for all analytes, were within the acceptable range of 85 % and 115 %. The average percent recoveries were all above 90 %. The method was successfully applied to clinical plasma samples from a Phase I study of daily oral Z-ENDX.
    Keywords:  Endoxifen; LC-MS/MS; Metabolite; Tamoxifen; Validation
  12. Se Pu. 2023 Apr;41(4): 339-347
      Xanthates with different alkyl groups, such as ethyl, propyl, butyl, and amyl groups, are widely used in large quantities in the mining flotation of metallic minerals. Xanthates enter environmental waters through mineral processing wastewater discharge and are ionized or hydrolyzed into ions or molecules of xanthic acids (XAs) in water. XAs endanger aquatic plants and animals, as well as human health. To the best of our knowledge, XA analysis is mainly limited to butyl xanthate. Moreover, the isomers and congeners of XAs cannot be determined separately using the existing methods. Herein, a novel method based on ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was established to separate and analyze five XAs, namely, ethyl-, isopropyl-, n-butyl-, isobutyl-, and amyl-XAs, in water. Water samples were filtered through a 0.22 μm hydrophilic polytetrafluoroethylene (PTFE) membrane and directly injected into the UPLC-MS/MS instrument. Separation was performed using a Waters Acquity UPLC BEH C18 column (100 mm×2.1 mm, 1.7 μm) with ammonia solution (pH 11)-acetonitrile (9∶1, v/v) as the mobile phase for isocratic elution. The five XAs were detected in the negative electrospray ionization (ESI-) and multiple reaction monitoring (MRM) modes. An internal standard method was used for quantification. The pretreatment and UPLC-MS/MS conditions were comprehensively optimized to achieve the separation and analysis of the five XAs via direct injection. The XAs showed negligible adsorption on hydrophobic PTFE, hydrophilic PTFE, hydrophilic polypropylene, and polypropylene membranes during filtration. However, the amyl-XA showed obvious adsorption on nylon and polyether sulfone membranes. The five XAs mainly formed [M-H]- parent ions in the ESI- mode and the main daughter ions obtained following collisional fragmentation depended on the alkyl groups of the XAs. Increasing the pH of the ammonia solution in the mobile phase to 11 led to the isomeric separation of n-butyl- and isobutyl-XAs. The optimized mobile phase inhibited the tailing of the chromatographic peak of amyl-XA and effectively improved all the chromatographic peak shapes of XAs. The BEH C18 column was selected as the chromatographic column owing to its better compatibility with high-pH solutions compared with the T3 C18 column. Preservation experiments conducted over 8 d showed that the concentration of all five XAs decreased over time at room temperature; among the XAs analyzed, the concentration of ethyl-XA revealed the most significant decrease. However, the recoveries of the five XAs at 4 and -20 ℃ remained high, ranging from 101% to 105% and from 100% to 106%, respectively, on the 8th day. The preservation observed with a high concentration of XAs was similar to that found with a low concentration. The preservation time was extended to 8 days at pH 11 and 4 ℃ away from the light. No significant matrix effects were observed for the five XA samples in surface water and groundwater, but industrial sewage exerted obvious matrix inhibitory effects on ethyl- and isopropyl-XAs. Owing to the short retention times of ethyl- and isopropyl-XAs, the co-fluxed interferents in the industrial sewage depressed the MS signals. The five XAs showed good linearity in the range of 0.25-100 μg/L, with correlation coefficients greater than 0.9996. The method detection limits were as low as 0.03-0.04 μg/L, and the intra- and inter-day precisions were 1.3%-2.1% and 3.3%-4.1%, respectively. The recoveries obtained under low, medium, and high spiked levels (1.00, 20.0, 80.0 μg/L) were 96.9%-133%, 100%-107%, and 104%-112%, respectively. The corresponding RSDs were 2.1%-3.0%, 0.4%-1.9%, and 0.4%-1.6%, respectively. The optimized method was successfully applied to the analysis of XAs in surface water, groundwater, and industrial sewage. The method could separate and detect various congeners and isomers of XAs without the need for cumbersome pretreatment processes, and its advantages include smaller sample requirements, simpler operation, higher sensitivity, and longer preservation time. The proposed technique presents excellent application potential in XA environmental monitoring and water evaluation, and mineral flotation studies.
    Keywords:  butyl xanthic acid; direct injection; ground water; industrial sewage; isomer; surface water; ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); xanthate
  13. J Chromatogr A. 2023 Mar 21. pii: S0021-9673(23)00149-8. [Epub ahead of print]1696 463923
      Isotope tracing assisted metabolic analysis is becoming a unique tool to understand metabolic regulation in cell biology and biomedical research. Targeted mass spectrometry analysis based on selected reaction monitoring (SRM) has been widely applied in isotope tracing experiment with the advantages of high sensitivity and broad linearity. However, its application for new pathway discovery is largely restrained by molecular coverage. To overcome this limitation, we describe a strategy called pseudo-targeted profiling of isotopic metabolomics (PtPIM) to expand the analysis of isotope labeled metabolites beyond the limit of known pathways and chemical standards. Pseudo-targeted metabolomics was first established with ion transitions and retention times transformed from high resolution (orbitrap) mass spectrometry. Isotope labeled MRM transitions were then generated according to chemical formulas of fragments, which were derived from accurate ion masses acquired by HRMS. An in-house software "PseudoIsoMRM" was developed to simulate isotope labeled ion transitions in batch mode and correct the interference of natural isotopologues. This PtPIM strategy was successfully applied to study 13C6-glucose traced HepG2 cells. As 313 molecules determined as analysis targets, a total of 4104 ion transitions were simulated to monitor 13C labeled metabolites in positive-negative switching mode of QQQ mass spectrometer with minimum dwell time of 0.3 ms achieved. A total of 68 metabolites covering glycolysis, TCA cycle, nucleotide biosynthesis, one-carbon metabolism and related derivatives were found to be labeled (> 2%) in HepG2 cells. Active pentose phosphate pathway was observed with diverse labeling status of glycolysis intermediates. Meanwhile, our PtPIM strategy revealed that rotenone severely suppressed mitochondrial function e.g. oxidative phosphorylation and fatty acid beta-oxidation. In this case, anaerobic respiration became the major source of energy metabolism by producing abundant lactate. Conclusively, the simulation based PtPIM method demonstrates a strategy to broaden metabolite coverage in isotope tracing analysis independent of standard chemicals.
    Keywords:  (13)C(6)-glucose tracing; Isotope labeling; Mass spectrometry; Pseudo-targeted Metabolomics; Simulated ion transitions
  14. J Chromatogr A. 2023 Mar 27. pii: S0021-9673(23)00180-2. [Epub ahead of print]1695 463954
      Developing efficient and comprehensive screening methods for prohibited substances in cosmetics is critical for ensuring the quality and safety of cosmetics used in everyday life. This study proposed a heart-cutting two-dimensional liquid chromatography-mass spectrometry (2D-LC-MS) method based on online diluting modulation for detecting multiclass prohibited substances in cosmetics. The 2D-LC-MS method combines HILIC and RPLC techniques. Compounds near the dead time that the first dimensional HILIC could not separate were transferred to the second dimensional RPLC by valve switch, achieving good separation with a wide range of polarities. Moreover, the online diluting modulation solved the problem of mobile phase incompatibility, realizing an excellent column-head focusing effect and reducing the loss of sensitivity. Besides, the first dimensional analysis did not restrict the flow rate of the second dimensional analysis owing to the diluting modulation. We demonstrated the 2D-LC-MS system by determining 126 prohibited substances in cosmetic products, including hormones, local anesthetics, anti-infectives, adrenergic agents, antihistamines, pesticides, and other chemicals. All correlation coefficients of the compounds were above 0.9950. The LODs and the LOQs ranged from 0.000259 ng/mL to 16.6 ng/mL and 0.000864 ng/mL to 55.3 ng/mL, respectively. The RSDs% for intra-day and inter-day precision were within 6% and 14%, respectively. Compared with conventional one-dimensional liquid chromatography methods, the established method expanded the analytical coverage of cosmetics-prohibited substances with reduced matrix effects for most compounds and improved sensitivity for polar analytes. The results indicated that the 2D-LC-MS method was a powerful tool for screening multiclass prohibited substances in cosmetics.
    Keywords:  2D-LC; Column-head focusing; Cosmetic; Diluting modulation; Prohibited substances
  15. J Vis Exp. 2023 03 17.
      Tibetan medicines are complex and contain numerous unknown compounds, making in-depth research on their molecular structures crucial. Liquid chromatography-electrospray ionization time-of-flight mass spectrometry (LC-ESI-TOF-MS) is commonly used to extract Tibetan medicine; however, many unpredictable unknown compounds remain after using the spectrum database. The present article developed a universal method for identifying components in Tibetan medicine using ion trap mass spectrometry (IT-MS). The method includes standardized and programmed protocols for sample preparation, MS setting, LC prerun, method establishment, MS acquisition, multiple-stage MS operation, and manual data analysis. Two representative compounds in the Tibetan medicine Abelmoschus manihot seeds were identified using multiple-stage fragmentation, with a detailed analysis of typical compound structures. In addition, the article discusses aspects such as ion mode selection, mobile phase adjustment, scanning range optimization, collision energy control, collision mode switchover, fragmentation factors, and limitations of the method. The developed standardized analysis method is universal and can be applied to unknown compounds in Tibetan medicine.
  16. Anal Bioanal Chem. 2023 Apr 05.
      In this work, we present an in situ droplet-based derivatization method for fast tissue lipid profiling at multiple isomer levels. On-tissue derivatization for isomer characterization was achieved in a droplet delivered by the TriVersa NanoMate LESA pipette. The derivatized lipids were then extracted and analyzed by the automated chip-based liquid extraction surface analysis (LESA) mass spectrometry (MS) followed by tandem MS to produce diagnostic fragment ions to reveal the lipid isomer structures. Three reactions, i.e., mCPBA epoxidation, photocycloaddition catalyzed by the photocatalyst Ir[dF(CF3)ppy]2(dtbbpy)PF6, and Mn(II) lipid adduction, were applied using the droplet-based derivatization to provide lipid characterization at carbon-carbon double-bond positional isomer and sn-positional isomer levels. Relative quantitation of both types of lipid isomers was also achieved based on diagnostic ion intensities. This method provides the flexibility of performing multiple derivatizations at different spots in the same functional region of an organ for orthogonal lipid isomer analysis using a single tissue slide. Lipid isomers were profiled in the cortex, cerebellum, thalamus, hippocampus, and midbrain of the mouse brain and 24 double-bond positional isomers and 16 sn-positional isomers showed various distributions in those regions. This droplet-based derivatization of tissue lipids allows fast profiling of multi-level isomer identification and quantitation and has great potential in tissue lipid studies requiring rapid sample-to-result turnovers.
    Keywords:  Droplet; Lipid isomer; Liquid extraction surface analysis; Mass spectrometry; On-tissue chemical derivatization
  17. Biomed Chromatogr. 2023 Apr 04. e5642
      The hexosamine biosynthesis pathway (HBP) is a glucose metabolism pathway that produces uridine diphosphate N-acetyl glucosamine (UDP-GlcNAc). Substantial changes in HBP, including elevated HBP flux and UDP-GlcNAc levels, are associated with cancer pathogenesis. Particularly, cancer cells expressing oncogenic Kirsten rat sarcoma virus (KRAS) are highly dependent on HBP for growth and survival. To differentiate between HBP metabolites in KRAS wild-type (WT) and mutant (MT) lung cancer cells, a simultaneous quantitative method for analyzing seven HPB metabolites was developed using ultra-high-performance liquid chromatography-tandem mass spectrometry. A simple method without complicated preparation steps, such as derivatization or isotope labeling, was optimized for the simultaneous analysis of highly hydrophilic HBP metabolites, and the developed method was successfully verified. The intra- and inter-day coefficients of variation were less than 15% for all HBP metabolites, and the recovery was 89.67-114.5%. All results of the validation list were in accordance with ICM M10 guidelines. Through this method, accurate quantification of HBP metabolites in lung cancer cells was performed, and it was confirmed that all HBP metabolites were upregulated in KRAS MT cells compared with KRAS WT lung cancer cells. We expect that this will be a useful tool for metabolic research on cancer and for the development of new drugs for cancer treatment.
    Keywords:  Hexosamine biosynthesis pathway; KRAS mutation; UPLC-MS/MS; ZIC-pHILIC column; quantitative analysis
  18. J Pharm Biomed Anal. 2023 Mar 25. pii: S0731-7085(23)00136-X. [Epub ahead of print]229 115367
      A rapid ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed and validated for the targeted analysis of 75 phenethylamines and their derivatives from the hair matrix. The monitored classes of phenethylamines included the 2C series, D series, N-benzyl derivatives, mescaline-derived compounds, MDMA analogs, and benzodifurans. Approximately 20 mg of hair was weighed and pulverized with 0.1% formic acid in methanol by cryogenic grinding. After ultrasonication, centrifugation, and filtration, the supernatant was analyzed by LC-MS/MS operating in the scheduled multiple reaction monitoring mode. Phenethylamines and their derivatives were separated in 13 min on a biphenyl column (2.6 µm, 100 Å, 100 × 3.0 mm) using a gradient eluting mobile phase composed of 0.1% formic acid in water and acetonitrile. The developed and validated method showed good selectivity, sensitivity (LOD: 0.5-10 pg/mg and LOQ: 1-20 pg/mg), linearity (R2 > 0.997), accuracy and precision (< 20%), and stability. The method also showed good recovery and acceptable matrix effects for most of the targeted compounds. This analytical approach was successfully applied for the identification and quantification of phenethylamines in hair from authentic forensic cases.
    Keywords:  Hair analysis; New psychoactive substance; Phenethylamine; UPLC-MS/MS
  19. Wellcome Open Res. 2022 ;7 262
      Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D- 1H, 13C-HSQC NMR spectra arising from 13C - 13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D- 1H, 13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.
    Keywords:  Metabolism; NMR spectroscopy; automated; independent component analysis; machine learning; metabolic tracing
  20. J Pharm Biomed Anal. 2023 Mar 23. pii: S0731-7085(23)00125-5. [Epub ahead of print]229 115356
      In this study, a reliable method was established for the absolute quantification of metabolite concentrations in human seminal plasma using ERETIC2, a quantification tool developed by Bruker based on the PULCON principle. The performance of the ERETIC2 was examined using an AVANCE III HD NMR spectrometer (600 MHz) equipped with a triple inverse 1.7 mm TXI probe in terms of some experimental parameters that may affect the accuracy and precision of the quantitative results. Then, the accuracy, precision, and repeatibility of ERETIC2 were determined using L-asparagine solutions at different concentrations. And it was evaluated by comparing it with the classical internal standard (IS) quantification method. The relative standard deviation (RSD) values for ERETIC2 were calculated in the range of 0.55-1.90% and the minimum recovery value was 99.9%, while the RSD values for the IS method were calculated in the range of 0.88-5.83% and recovery value was minimum 91.0%. Besides, the RSD values of the inter-day precisions for the ERETIC2 and IS methods were obtained to be in the range of 1.25 - 3.03% and 0.97 - 3.46%, respectively. Finally, the concentration values of seminal plasma metabolites were determined using different pulse programs with both methods for samples obtained from normozoospermic control and azoospermic patient groups. The results proved that this quantification method developed using NMR spectroscopy is easy to use in complex sample systems such as biological fluids and is a good alternative to the classical internal standard method in terms of accuracy and sensitivity. In addition, the improvement of the spectral resolution and sensitivity with the microcoil probe technology and the possibility of analyzing with minimum sample quantities has contributed positively to the results of this method.
    Keywords:  ERETIC2; Metabolite concentration; NMR spectroscopy; PULCON; Quantification
  21. J Am Soc Mass Spectrom. 2023 Apr 02.
      Mass spectrometry analysis can be performed by introducing samples directly to mass spectrometry, allowing the increase of the analysis throughput; however, some disadvantages of direct-to-mass spectrometry analysis include susceptibility to matrix effects and risk of instrument contamination from inadequate sample preparation. Solid-phase microextraction is one of the most suitable sample preparation methods for direct-to-mass spectrometry analysis, as it offers matrix-compatible coatings which ensure analyte enrichment with minimal or no interference from matrix. One of the ways solid-phase microextraction can be coupled directly to mass spectrometry is via a microfluidic open interface. This manuscript reports improvements made to the initial microfluidic open interface design, where the system components have been simplified to mostly commercially available materials. In addition, the analysis of samples has been automated by implementing software that fully controls the analysis workflow, where the washing procedure is optimized to completely reduce the carryover. Herein, the extraction and desorption time profiles from thin and thick SPME devices was studied where the overall workflow consisted of high-throughput sample preparation of 1.3 min per 96 samples and <1 min per sample instrumental analysis.
  22. J Sep Sci. 2023 Apr 04. e2300084
      Direct oral anticoagulants are widely used in many indications to prevent thromboembolic events. Routine therapeutic monitoring is not required; however, there is increasing evidence suggesting the benefit of plasma level measurement in some situations. In addition, laboratory monitoring might help improve patient and drug non-compliance and thus individualize therapy. In the present study, we developed a sensitive and high throughput ultra-high-performance liquid chromatography-tandem mass spectrometry method for simultaneous quantification of apixaban, dabigatran, edoxaban and rivaroxaban in human plasma. A one-step extraction procedure in 96-well formate for phospholipid and protein removal was used for sample pre-treatment, and analytes were separated using gradient elution over 4.2 min. Analytes were detected on a triple quadrupole tandem mass spectrometer by multiple reaction monitoring mode. The method was validated according to the European Medicine Agency guideline for the selectivity, linearity and lower limit of detection, precision and accuracy, matrix effects, extraction recovery, carryover, dilution integrity and stability over a concentration range of 3.0-1000 ng/mL for all analytes. The validated method was applied to real clinical samples of patients treated with one of the drugs. Therefore, we can conclude that our method is suitable for therapeutic drug monitoring of direct oral anticoagulants. This article is protected by copyright. All rights reserved.
    Keywords:  direct oral anticoagulants; human plasma; tandem mass spectrometry; therapeutic drug monitoring
  23. J Pharm Biomed Anal. 2023 Mar 31. pii: S0731-7085(23)00149-8. [Epub ahead of print]229 115380
      Quantification of substances in biofluid samples (e.g., urine, blood, and cerebrospinal fluids) are useful for clinical diagnosis. In current study, a rapid and green strategy by coupling in-syringe kapok fiber-supported liquid-phase microextraction with flow-injection mass spectrometry was proposed. The natural kapok fiber was used as an oily extraction solvent (e.g., n-octanol) support material, and an in-syringe extraction device was conveniently constructed. The whole extraction processes, including sampling, washing and desorption, were conveniently conducted by simply pulling/pushing the syringe plunger, enabling rapid analyte enrichment and sample purification. The follow-up flow injection-mass spectrometry detection enabled rapid and high throughput analysis. As an example, the proposed method was applied to analyze antidepressants in plasma/urine, showing satisfied linearities (R2 ≥0.993) in ranges of 0.2-1000 ng/mL. By employing the in-syringe extraction method prior to flow injection-mass spectrometry detection, the LOQs in plasma and urine were reduced by 25-80 folds and 5-25 folds, respectively. Besides, by employing ethanol and 80% ethanol as the desorption solvent and carrier solvent, respectively, the analytical method showed excellent greenness. In general, the integrated method provides a promising choice for rapid and green biofluid analysis.
    Keywords:  Antidepressants; Biofluid; Flow injection; Kapok fiber; Mass spectrometry; Supported liquid-phase microextraction