bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2022‒10‒16
fourteen papers selected by
Sofia Costa

  1. Anal Chem. 2022 Oct 11.
      Octadecanoids are broadly defined as oxylipins (i.e., lipid mediators) derived from 18-carbon fatty acids. In contrast to the well-studied eicosanoids, there is a lack of analytical methods for octadecanoids, hampering further investigations in the field. We developed an integrated workflow combining chiral separation by supercritical fluid chromatography (SFC) and reversed-phase liquid chromatography (LC) coupled to tandem mass spectrometry detection for quantification of a broad panel of octadecanoids. The platform includes 70 custom-synthesized analytical and internal standards to extend the coverage of the octadecanoid synthetic pathways. A total of 103 octadecanoids could be separated by chiral SFC and complex enantioseparations could be performed in <13 min, while the achiral LC method separated 67 octadecanoids in 13.5 min. The LC method provided a robust complementary approach with greater sensitivity relative to the SFC method. Both methods were validated in solvent and surrogate matrix in terms of linearity, lower limits of quantification (LLOQ), recovery, accuracy, precision, and matrix effects. Instrumental linearity was good for both methods (R2 > 0.995) and LLOQ ranged from 0.03 to 6.00 ng/mL for SFC and 0.01 to 1.25 ng/mL for LC. The average accuracy in the solvent and surrogate matrix ranged from 89 to 109% in SFC and from 106 to 220% in LC, whereas coefficients of variation (CV) were <14% (at medium and high concentrations) and 26% (at low concentrations). Validation in the surrogate matrix showed negligible matrix effects (<16% for all analytes), and average recoveries ranged from 71 to 83%. The combined methods provide a platform to investigate the biological activity of octadecanoids and expand our understanding of these little-studied compounds.
  2. J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Oct 03. pii: S1570-0232(22)00391-9. [Epub ahead of print]1211 123487
      Beta 2-microglobulin (B2M) is a commonly used detection index in clinical laboratories. Currently, it is used as a sensitive indicator for the early detection of kidney disease. Immunoassay is the most commonly used method for B2M detection in clinical practice. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has changed the face of laboratory testing by providing high-throughput analysis with better specificity than detection methods using only antibodies. An isotope-dilution LC-MS/MS (ID-LC-MS/MS) method was developed for serum B2M quantification. After B2M denaturation, reduction and alkylation of cysteine residues, trypsin was added for digestion of B2M. Then, it was purified by a solid-phase extraction column, and the sample was injected into a high-performance LC-MS/MS for measurement. A signature peptide (VNHVTLSQPK) was selected as a surrogate for B2M. A stable isotope-labeled peptide (VNHVT[13C615N]LSQP) was used as the internal standard to quantify B2M based on the calibration curve method. The linear range of serum B2M calibration curve was from 0.25 to 40 mg/L. The limit of quantification was 0.25 mg/L, and limit of detection was 0.06 mg/L. At different concentrations of serum B2M, the precision (coefficients of variation, CV%) ranged from 1.47% to 3.97%, and accuracy (relative error, RE%) was within -3.15% and 6.80% of nominal values. The applicability and reliability of the method were verified by measuring B2M in the ERM-DA470k/IFCC and serum samples. The validated LC-MS/MS method was successfully applied to a clinical study involving quantification of serum B2M in patients with acute renal insufficiency and healthy individuals. Deming analysis showed that the ID-LC-MS/MS and immunoassay were in good agreement. The LC-MS/MS method we developed is sensitive and reliable for the absolute quantification of serum B2M.
    Keywords:  Beta 2-microglobulin; ID-LC-MS/MS; Quantification; Sensitive; Validation
  3. Anal Chim Acta. 2022 Oct 23. pii: S0003-2670(22)00990-4. [Epub ahead of print]1231 340419
      Imaging the distribution of metabolites is very powerful in diagnostics but it is also employed in fundamental research. Although NMR spectroscopy is well established for determining metabolic profiles of biological samples, its application is limited to magnetic resonance imaging that can produce images of larger structures, but the number of detectable metabolites is very low. Mass spectrometry imaging on the other hand is well established with pixel sizes in the μm range. This limits the analysis of larger structures like tissue sections and detection of metabolites depends on their ionization properties. High resolution NMR metabolomics could complement these methods. However, this is prevented due to time consuming extraction procedures. To overcome these limitations, the following protocol was established and applied to two different ham slices: sampling is directly done into the NMR tube and after extraction of polar and non-polar metabolites in the NMR tube, slice selective NMR spectra are acquired. Multivariate analysis (PCA) of the NMR-spectra and subsequent visualization of the differences correlate well with structures visible in the ham slices. The proposed protocol can be used for metabolic imaging and could complement other imaging methods.
    Keywords:  Imaging; Metabolic imaging; Metabolomics; NMR spectroscopy; Slice selection
  4. STAR Protoc. 2022 Oct 13. pii: S2666-1667(22)00649-9. [Epub ahead of print]3(4): 101769
      We describe a protocol for measuring phospholipid class and fatty acid composition in the budding yeast Saccharomyces cerevisiae using a liquid chromatography-mass spectrometry (LC-MS)-based approach. We compile a mass spectral-retention time library verified for major phospholipids in the budding yeast and showcase the profiling process of phospholipid compositions in mutants with defective syntheses of phosphatidylethanolamine (PE) and phosphatidylcholine (PC). We further provide methods for extracting and quantifying phospholipids in mammalian systems. For complete details on the use and execution of this protocol, please refer to Fang et al. (2022).
    Keywords:  Cell biology; Mass spectrometry; Metabolomics; Model organisms
  5. J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Oct 07. pii: S1570-0232(22)00398-1. [Epub ahead of print]1211 123494
      Bioanalytical assay development and validation procedures were performed to quantify antiprotozoal drug paromomycin in human skin tissue by ultra-high performance liquid chromatography coupled to tandem mass spectrometry. Paromomycin, an aminoglycoside drug, is administered intra-muscularly and used in the treatment of multiple clinical presentations of the neglected tropical disease leishmaniasis. It is currently studied in the treatment of post-kala-azar dermal leishmaniasis, a disease where the Leishmania parasites divide and reside in the skin. We present a target-site bioanalytical method to accurately quantify paromomycin in human skin tissue, with the clinical purpose of quantifying paromomycin in skin biopsies from post-kala-azar dermal leishmaniasis patients originating from Sudan. Enzymatic digestion using collagenase A incubated at 37 °C overnight was employed as homogenization method to produce skin tissue homogenates. Further sample preparation was performed by protein precipitation using trichloroacetic acid and a dilution step. Final extracts were injected onto a C18 analytical column and isocratic heptafluorobutyric acid ion-pair separation and elution were employed. The chromatography system was coupled to a triple quadrupole mass spectrometer for detection. The method was validated in digestion solution over a linear range from 5 to 1000 ng/mL (r2 ≥ 0.9967) with the assay performance of accuracy and precision within acceptable criteria values as stated by the EMA guidelines. Furthermore, matrix effects were observed in human skin tissue and were corrected by the multiple deuterated paromomycin internal standard. No substantial IS-normalized matrix effect was detected along with relatively high sample preparation recovery. Consequently, digestion solution matrix serving as the preparation of calibration standards can be used as surrogate matrix for human skin tissue, which is convenient given the limited availability of control matrix. Finally, paromomycin was accurately quantified in skin of post-kala-azar dermal leishmaniasis patients originating from clinical trials in Sudan.
    Keywords:  Assay: Bioanalytical validation; Human skin tissue; Leishmaniasis; Paromomycin; Tandem mass spectrometry
  6. Anal Chem. 2022 Oct 12.
      Mass spectrometry imaging (MSI) maps the spatial distributions of chemicals on surfaces. MSI requires improvements in throughput and spatial resolution, and often one is compromised for the other. In microprobe-mode MSI, improvements in spatial resolution increase the imaging time quadratically, thus limiting the use of high spatial resolution MSI for large areas or sample cohorts and time-sensitive measurements. Here, we bypass this quadratic relationship by combining a Timepix3 detector with a continuously sampling secondary ion mass spectrometry mass microscope. By reconstructing the data into large-field mass images, this new method, fast mass microscopy, enables orders of magnitude higher throughput than conventional MSI albeit yet at lower mass resolution. We acquired submicron, gigapixel images of fingerprints and rat tissue at acquisition speeds of 600,000 and 15,500 pixels s-1, respectively. For the first image, a comparable microprobe-mode measurement would take more than 2 months, whereas our approach took 33.3 min.
  7. Talanta. 2022 Sep 22. pii: S0039-9140(22)00753-6. [Epub ahead of print]253 123957
      N-acyl homoserine lactones (N-HLs) are signaling molecules synthesized by gram-negative bacteria to communicate in a process called quorum sensing. Most reported methods for the analysis of N-HLs, which are chiral molecules, do not distinguish between enantiomers. Typical examples include biosensors, liquid chromatography with UV detection, gas chromatography coupled with a mass spectrometer (GC-MS) and liquid chromatography coupled with mass spectrometer (LC-MS). Recently, the production of both D,L-N-HLs have been reported in Vibrio fischeri and Burkholderia cepacia. Concentrations of the D-N-HLs were found at the limit of quantification for the employed method. Therefore, for further studies of the role of the D-N-HLs in bacterial physiology, more sensitive, reliable, and selective analytical methods are necessary. In this work, such comprehensive chiral analytical methods for the identification and determination of 18 N-HLs using solid phase extraction followed by GC-MS/MS and LC-MS/MS analyses were developed. Extraction recoveries for the more hydrophilic C4 N-HLs were <10% of all other N-HLs, thus offering a possible explanation as to their lack of detection in previous studies. The chiral separations of all 18 N-HLs derivatives were accomplished by the complementary GC-MS/MS and LC-MS/MS methods. The limit of detection for LC-MS/MS method was as low as 1 ppb. The limit of detection for the GC-MS/MS method was found to be one to three orders of magnitude higher than the LC-MS/MS method. Due to the high extraction recovery and a preconcentration factor of 100, concentrations as low as 10 ppt can be detected by LC-MS/MS in biological samples. The LC-MS/MS approach provided greater enantioselectivity for the larger, more hydrophobic N-HLs while GC-MS/MS provided better enantioselectivity for the smaller N-HLs.
    Keywords:  Chiral separations; Mass spectrometry; N-acyl homoserine lactones; Quorum sensing; Solid-phase extraction
  8. Xenobiotica. 2022 Oct 13. 1-28
      Understanding compound metabolism in early drug discovery aids medicinal chemistry in designing molecules with improved safety and ADME properties. While advancements in metabolite prediction brings increasedconfidence, structural decisions require experimental data. In vitro metabolism studies using liquid chromatography and high-resolution mass spectrometry (LC-MS) are generally resource intensive and performed on very few compounds, limiting the chemical space that can be examined.Here, we describe a novel metabolism strategy increasing compound throughput using residual in vitro clearance samples conducted at drug concentrations of 0.5 µM. Analysis by robust UHPLC separation and accurate-mass MS detection ensures major metabolites are identified from a single injection. In silico prediction (parent cLogD) tailors chromatographic conditions, with data-dependent MS/MS targeting predicted metabolites. Software-assisted data mining, structure elucidation and automatic reporting are used.Confidence in the globally-aligned workflow is demonstrated with sixteen marketed drugs. The approach is now implemented routinely across our laboratories. To date, the success rate for identification of at least one major metabolite is 85%. The utility of these data has been demonstrated across multiple projects, allowing earlier medicinal chemistry decisions to increase efficiency and impact of the design-make-test cycle; thus improving the translatability of early in vitro metabolism data.
    Keywords:  biotransformation; chemical design; datamining software; drug discovery; high-resolution mass spectrometry (HRMS) ; high-throughput; in silico prediction; in vitro translatability; intrinsic clearance; quan-qual
  9. J Am Soc Mass Spectrom. 2022 Oct 11.
      While various mass spectrometric approaches have been applied to lipid analysis, unraveling the extensive structural diversity of lipids remains a significant challenge. Notably, these approaches often fail to differentiate between isomeric lipids─a challenge that is particularly acute for branched-chain fatty acids (FAs) that often share similar (or identical) mass spectra to their straight-chain isomers. Here, we utilize charge-switching strategies that combine ligated magnesium dications with deprotonated fatty acid anions. Subsequent activation of these charge inverted anions yields mass spectra that differentiate anteiso-branched- from straight-chain and iso-branched-chain FA isomers with the predictable fragmentation enabling de novo assignment of anteiso branch points. The application of these charge-inversion chemistries in both gas- and solution-phase modalities is demonstrated to assign the position of anteiso-methyl branch-points in FAs and, with the aid of liquid chromatography, can be extended to de novo assignment of additional branching sites via predictable fragmentation patterns as methyl branching site(s) move closer to the carboxyl carbon. The gas-phase approach is shown to be compatible with top-down structure elucidation of complex lipids such as phosphatidylcholines, while the integration of solution-phase charge-inversion with reversed phase liquid chromatography enables separation and unambiguous identification of FA structures within isomeric mixtures. Taken together, the presented charge-switching MS-based technique, in combination with liquid chromatography, enables the structural identification of branched-chain FA without the requirement of authentic methyl-branched FA reference standards.
  10. Talanta. 2022 Sep 24. pii: S0039-9140(22)00761-5. [Epub ahead of print]253 123965
      The sensitive and simultaneous measurement of multiple neurotransmitters in microdialysate (MD) of freely moving mice is a prerequisite to study neurochemical imbalances in specific brain regions. The quantitative analysis of 16 neurotransmitters and metabolites, including serotonin (5-HT), 5-hydroxyindoleacetic acid (5-HIAA), melatonin (ME), dopamine (DA), levodopa (l-DOPA), 3-methoxytyramine (3-MT), norepinephrine (NE), epinephrine (EP), homovanillinic acid (HVA), acetylcholine (ACh), deoxy carnitine (iso-ACh), choline (Ch), and ɣ-aminobutyric acid (GABA), adenosine (ADE), glutamine (Gln), and glutamic acid (Glu) was achieved within a chromatographic separation time of 6.5 min by the application of a biphenyl column coupled to an API-QTrap 5500 (AB SCIEX) mass spectrometer. Optimized chromatographic separation as well as high sensitivity allow the simultaneous analysis and precise quantification of 16 neurotransmitters and metabolites in artificial cerebrospinal fluid (CSF). Sample preparation procedure consisted of simply adding isotopically labeled internal standard solution to the microdialysis sample. The limits of detection in aCSF ranged from 0.025 pg (Ch) to 9.75 pg (Gln) and 85.5 pg (HVA) on column. Recoveries were between 83 and 111% for neurotransmitter concentrations from 0.6 to 45 ng/ml or 200 ng/ml with a mean intra-day and inter-day coefficient of variation of 7.6% and 11.2%, respectively. Basal extracellular concentrations of the following analytes: 5-HT, 5-HIAA, ME, DA, 3-MT, HVA, ACh, iso-ACh, Ch, GABA, ADE, Gln, and Glu were determined in the striatum of mice with a MD flow rate of 0.5 μl/min. This LC-MS/MS method leads to an accurate quantification of ACh and its isobaric structure iso-ACh, which were detected in the MD samples at ratios of 1:8.6. The main advantage of the high sensitivity is the miniaturization of the MD protocol with short sample collection times and volumes down to 5 μl, which makes this method suitable for pharmacological intervention and optogenetic studies to detect neurochemical changes in vivo.
    Keywords:  Basal values; Deoxy carnitine; LC-MS/MS; Murine microdialysis; Neurochemistry; Neurotransmitter
  11. J Biol Chem. 2022 Oct 09. pii: S0021-9258(22)01029-8. [Epub ahead of print] 102586
      Metabolic networks are complex, intersecting, and composed of numerous enzyme-catalyzed biochemical reactions that transfer various molecular moieties among metabolites. Thus, robust reconstruction of metabolic networks requires metabolite moieties to be tracked, which cannot be readily achieved with mass spectrometry (MS) alone. We previously developed an Ion Chromatography (IC)-ultrahigh resolution (UHR)-MS1/data independent (DI)-MS2 method to track the simultaneous incorporation of the heavy isotopes 13C and 15N into the moieties of purine/pyrimidine nucleotides in mammalian cells. UHR-MS1 resolves and counts multiple tracer atoms in intact metabolites while DI-tandem MS (MS2) determines isotopic enrichment in their moieties without concern for the numerous mass isotopologue source ions to be fragmented. Together, they enabled rigorous MS-based reconstruction of metabolic networks at specific enzyme levels. We have expanded this approach to trace the labeled atom fate of [13C6]-glucose in 3D A549 spheroids in response to the anti-cancer agent selenite and that of [13C5,15N2]-glutamine in 2D BEAS-2B cells in response to arsenite transformation. We deduced altered activities of specific enzymes in the Krebs cycle, pentose phosphate pathway, gluconeogenesis, and UDP N-acetylglucosamine synthesis pathways elicited by the stressors. These metabolic details help elucidate the resistance mechanism of 3D versus 2D A549 cultures to selenite and metabolic reprogramming that can mediate the transformation of BEAS2B cells by arsenite.
    Keywords:  Selenite; [(13)C(5),(15)N(2)]-glutamine; [(13)C(6)]-glucose; arsenite; metabolic pathway reconstruction; positional isotopologues; stable isotope resolved metabolomics (SIRM)
  12. Molecules. 2022 Sep 30. pii: 6466. [Epub ahead of print]27(19):
      Mass spectrometry (MS) has become the central technique that is extensively used for the analysis of molecular structures of unknown compounds in the gas phase. It manipulates the molecules by converting them into ions using various ionization sources. With high-resolution MS, accurate molecular weights (MW) of the intact molecular ions can be measured so that they can be assigned a molecular formula with high confidence. Furthermore, the application of tandem MS has enabled detailed structural characterization by breaking the intact molecular ions and protonated or deprotonated molecules into key fragment ions. This approach is not only used for the structural elucidation of small molecules (MW &lt; 2000 Da), but also crucial biopolymers such as proteins and polypeptides; therefore, MS has been extensively used in multiomics studies for revealing the structures and functions of important biomolecules and their interactions with each other. The high sensitivity of MS has enabled the analysis of low-level analytes in complex matrices. It is also a versatile technique that can be coupled with separation techniques, including chromatography and ion mobility, and many other analytical instruments such as NMR. In this review, we aim to focus on the technical advances of MS-based structural elucidation methods over the past five years, and provide an overview of their applications in complex mixture analysis. We hope this review can be of interest for a wide range of audiences who may not have extensive experience in MS-based techniques.
    Keywords:  gas-phase ion chemistry; molecular characterization; omics; structural elucidation; tandem mass spectrometry
  13. Talanta. 2022 Oct 04. pii: S0039-9140(22)00782-2. [Epub ahead of print]253 123986
      Synthetic cathinones, a subclass of new psychoactive substances, have gained high popularity on the recreational drugs market over the past years. These drugs typically have a chiral center, so they may exist as two stereoisomers. Therefore the pharmacological, pharmacokinetic or metabolic properties of their enantiomers are expected to differ. However, these drugs are often synthesized and sold as a racemic mixture, and as a consequence, differentiation of their (R)- and (S)- enantiomers is relevant in clinical and forensic toxicology. Information about single enantiomers of synthetic cathinones is relatively scarce due to challenges of their chiral analysis. Hence, a sensitive and reliable liquid chromatography-tandem mass spectrometry method was developed and validated for the chiral separation and quantification of four synthetic cathinones in human whole blood samples. The method was fully validated in terms of linearity, limit of detection, limit of quantification, bias, precision, carryover, interferences, matrix effects, recovery and processed sample stability and successfully applied to evaluate the stability as well as enantioselective degradation of synthetic cathinones enantiomers under various storage conditions. For most of the analytes, significant enantioselective degradation was observed when stored at room temperature or refrigerated, with the E2-enantiomers observed to more rapidly degrade under both conditions. This is the first report concerning the stability and enantioselective degradation of synthetic cathinone enantiomers in whole blood. Moreover, the inversion study demonstrated enantiomeric inversion of R-(-)- and S-(+)-methylenedioxypyrovalerone (MDPV) in human whole blood and methanolic solution.
    Keywords:  Chiral LC-MS/MS; Stability; Synthetic cathinones; Whole blood
  14. J Chromatogr A. 2022 Sep 23. pii: S0021-9673(22)00721-X. [Epub ahead of print]1683 463529
      In this article, a serially connected dual column liquid chromatography-tandem mass spectrometry (LC-MS/MS) method is described for the simultaneous separation and enantioseparation of proteinogenic amino acids. For this purpose, different achiral and chiral stationary phases (CSP) and mobile phase compositions have been tested. As a result of the optimization studies, the best enatioseparation for amino acids were achieved with a combination of zwitterionic and crown ether stationary phases using a gradient of two mobile phases: A (water:TFA 99.5:0.5, % v/v) and B (acetonitrile:ethanol:TFA 85:15:0.5, % v/v/v). The developed method provided simultaneous enantioseparation of all proteinogenic amino acids under this study including isomeric and isobaric ones except for proline. The method was successfully applied to human lung adenocarcinoma cells (A549) and healthy human lung epithelial cells (BEAS-2B) cultivated with d-amino acid containing cocktails in order to evaluate d-amino acids transfer rate in normal and cancer lines. Thed/l amino acid ratios were different in cancer and normal cell lines cultivated as mentioned above for aspartic acid, cysteine, methionine, phenylalanine, and serine.
    Keywords:  Chiral crown ether; Dual column; Enantioseparation; Native amino acids; ZIC-HILIC