bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2022‒05‒08
fifteen papers selected by
Sofia Costa
Icahn School of Medicine at Mount Sinai

  1. J Lipid Res. 2022 Apr 27. pii: S0022-2275(22)00051-7. [Epub ahead of print] 100218
      One challenge remaining in the methodology of lipidomics is to determine and quantify the precise content of complex lipidomes to the exact molecular species. Often, multiple methods are needed to achieve sufficient lipidomic coverage to make these determinations. Multiplexed targeted assays offer a practical alternative to enable quantitative lipidomics amenable to quality control standards within a scalable platform. Herein, we developed a multiplexed normal phase liquid chromatography-hydrophilic interaction chromatography multiple reaction monitoring (NPLC-HILIC MRM) method that quantifies lipid molecular species across over 20 lipid classes spanning wide polarities in a single 20-minute run. Analytical challenges such as in-source fragmentation, isomer separations, and concentration dynamics were addressed to ensure confidence in selectivity, quantification, and reproducibility. Utilizing multiple MS/MS product ions per lipid species not only improved the confidence of lipid identification, but also enabled the determination of relative abundances of positional isomers in samples. Lipid class-based calibration curves were applied to interpolate lipid concentrations and guide sample dilution. Analytical validation was performed following FDA Bioanalytical Method Validation Guidance for Industry. We demonstrate repeatable and robust quantitation of 900 lipid species measured in NIST-SRM-1950 plasma with over 700 lipids, achieving inter-assay variability below 25%. Using this method, we identified mice plasma lipidome alterations following treating of mice with a potent glucosylceramide synthase inhibitor, Benzoxazole 1 (BZ1). We observed expected reductions in glycosphingolipids and report additional alterations beyond glycosphingolipid metabolism. Our platform provides a streamlined strategy for lipid biomarker discovery that can be readily adapted for additional analytes and deployed across multiple labs.
    Keywords:  Benzoxazole 1; FDA bioanalytical method validation guidance for industry; glucosylceramide synthase; glycosphingolipid metabolism; hydrophilic interaction chromatography (HILIC); normal phase liquid chromatography (NPLC); quantitative lipidomics; scheduled MRM; targeted lipidomics; triple quadrupole mass spectrometry
  2. Front Plant Sci. 2022 ;13 854842
      Natural products produced by plants are one of the most investigated natural sources, which substantially contributed to the development of the natural products field. Even though these compounds are widely explored, the literature still lacks comprehensive investigations aiming to explore the evolution of secondary metabolites produced by plants, especially if classical methodologies are employed. The development of sensitive hyphenated techniques and computational tools for data processing has enabled the study of large datasets, being valuable assets for chemosystematic studies. Here, we describe a strategy for chemotaxonomic investigations using the Malpighiaceae botanical family as a model. Our workflow was based on MS/MS untargeted metabolomics, spectral searches, and recently described in silico classification tools, which were mapped into the latest molecular phylogeny accepted for this family. The metabolomic analysis revealed that different ionization modes and extraction protocols significantly impacted the chemical profiles, influencing the chemotaxonomic results. Spectral searches within public databases revealed several clades or genera-specific molecular families, being potential chemical markers for these taxa, while the in silico classification tools were able to expand the Malpighiaceae chemical space. The classes putatively annotated were used for ancestral character reconstructions, which recovered several classes of metabolites as homoplasies (i.e., non-exclusive) or synapomorphies (i.e., exclusive) for all sampled clades and genera. Our workflow combines several approaches to perform a comprehensive evolutionary chemical study. We expect it to be used on further chemotaxonomic investigations to expand chemical knowledge and reveal biological insights for compounds classes in different biological groups.
    Keywords:  ancestral character reconstruction; chemotaxonomy; evolution; malpighiales; mass spectrometry; metabolite annotation; metabolomics; systematics
  3. Cancer Biomark. 2022 ;33(4): 437-447
      Characterization of cellular metabolic states is a technical challenge in biomedicine. Cellular heterogeneity caused by inherent diversity in expression of metabolic enzymes or due to sensitivity of metabolic reactions to perturbations, necessitates single cell analysis of metabolism. Heterogeneity is typically seen in cancer and thus, single-cell metabolomics is expectedly useful in studying cancer progression, metastasis, and variations in cancer drug response. However, low sample volumes and analyte concentrations limit detection of critically important metabolites. Capillary microsampling-based mass spectrometry approaches are emerging as a promising solution for achieving single-cell omics. Herein, we focus on the recent advances in capillary microsampling-based mass spectrometry techniques for single-cell metabolomics. We discuss recent technical developments and applications to cancer medicine and drug discovery.
    Keywords:  Capillary microsampling-based single-cell analysis; cell-to-cell variability; mass spectrometry; metabolomics; single-cell applications
  4. STAR Protoc. 2022 Jun 17. 3(2): 101345
      Analyzing the metabolic dependencies of tumor cells is vital for cancer diagnosis and treatment. Here, we describe a protocol for 13C-stable glucose and glutamine isotope tracing in mice HER2+ breast cancer brain metastatic lesions. We describe how to inject cancer cells intracardially to generate brain metastatic lesions in mice. We then detail how to perform 13C-stable isotope infusion in mice with established brain metastasis. Finally, we outline steps for sample collection, processing for metabolite extraction, and analyzing mass spectrometry data. For complete details on the use and execution of this protocol, please refer to Parida et al. (2022).
    Keywords:  Cancer; Cell Biology; Cell culture; Mass Spectrometry; Metabolism; Metabolomics
  5. Pathology. 2022 Apr 29. pii: S0031-3025(22)00121-0. [Epub ahead of print]
      Asymmetric dimethylguanidino valeric acid (ADGV), asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA) are three arginine metabolites which have utility in the assessment of cardiovascular disease, renal disease and non-alcoholic fatty liver disease (NAFLD). Translation of these research metabolomic markers into routine clinical use requires the development of robust assays with appropriately assessed preanalytical variables and traceable clinical reference intervals. A hydrophilic interaction liquid chromatography (HILIC) tandem mass spectrometry (LC-MS/MS) method for the simultaneous quantification of ADGV, ADMA and SDMA was developed. Sample stability and collection conditions were scrutinised to determine any preanalytical factors that could affect quantification under routine laboratory conditions. Patient samples from 120 males and 120 females were used to derive preliminary reference intervals. All three analytes were quantifiable in human plasma using unique MS/MS transitions. The analytes were stable for up to a week once separated from red cells, though reduced stability was observed upon extraction of the analytes from plasma. The assay was linear for concentration of ADGV between 1.6 nmol/L and 200 nmol/L and for ADMA and SDMA between 0.1 μmol/L and 4.0 μmol/L. The accuracy for all analytes was 97-103% and interday and intraday imprecisions (coefficients of variation) were less than 10%. ADGV concentrations were noted to be lower in the female reference population when compared to males. The analytical method shows excellent performance and is sufficiently robust to be used in the clinical investigation of cardiovascular disease and NAFLD.
    Keywords:  ADGV; ADMA; LC-MS/MS; SDMA; cardiometabolic risk; dimethylguanidino valeric acid
  6. Nat Commun. 2022 May 06. 13(1): 2510
      Interrelating small molecules according to their aligned fragmentation spectra is central to tandem mass spectrometry-based untargeted metabolomics. Current alignment algorithms do not provide statistical significance and compounds that have multiple delocalized structural differences and therefore often fail to have their fragment ions aligned. Here we align fragmentation spectra with both statistical significance and allowance for multiple chemical differences using Significant Interrelation of MS/MS Ions via Laplacian Embedding (SIMILE). SIMILE yields spectral alignment inferred structural connections in molecular networks that are not found with cosine-based scoring algorithms. In addition, it is now possible to rank spectral alignments based on p-values in the exploration of structural relationships between compounds and enhance the chemical connectivity that can be obtained with molecular networking.
  7. Nat Commun. 2022 May 03. 13(1): 2424
      Mass spectrometry is an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated into RNA therapeutics. To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. The main features of Pytheas are flexible handling of isotope labeling and RNA modifications, with false discovery rate statistical validation based on sequence decoys. We demonstrate bottom-up mass spectrometry characterization of diverse RNA sequences, with broad applications in the biology of stable RNAs, and quality control of RNA therapeutics and mRNA vaccines.
  8. Anal Bioanal Chem. 2022 May 02.
      The determination of vitamin D metabolites as status marker or for diagnostic purposes is almost entirely conducted from blood serum or plasma. Other biological matrices, however, have also interested researchers, for two main reasons: (1) alternative matrices may allow non-invasive sampling, permit easier sample transfer and require less demanding storage conditions; and (2) the levels of vitamin D metabolites in other body compartments may further aid the understanding of vitamin D metabolism and function. Thus, the development of reliable and efficient sample preparation protocols for sample matrices other than serum/plasma, which will remove potential interferences and selectively extract the targeted metabolites, is of great importance. This review summarizes sample preparation methods for measurement of vitamin D metabolites using liquid chromatography-(tandem)mass spectrometry in more than ten different human tissues, including hair, saliva, adipose tissue, brain and others.
    Keywords:  25-Hydroxyvitamin D3; Alternative/non-conventional biological samples; LC–MS/MS; Sample preparation; Vitamin D metabolites
  9. RSC Adv. 2020 May 10. 10(31): 18305-18314
      Neurotransmitters (NTs) are specific endogenous metabolites that act as "messengers" in synaptic transmission and are widely distributed in the central nervous system. Olanzapine (OLZ), a first-line antipsychotic drug, plays a key role in sedation and hypnosis, but, it presents clinical problems with a narrow therapeutic window, large individual differences and serious adverse effects, as well as an unclear mechanism in vivo. Herein, a simultaneous targeted NT quantification and nontargeted metabolomics method was developed and validated for pharmacometabolomics analysis of OLZ by using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS). Considering the low physiological concentrations of NTs, a full MS scan and target selective ion monitoring (tSIM) scan were combined for nontargeted metabolomics and targeted NT quantification, respectively. By using this strategy, NTs at a very low physiological concentration can be accurately detected and quantified in biological samples by tSIM scans. Moreover, simultaneously nontargeted profiling was also achieved by the full MS scan. The newly established UPLC-HRMS method was further used for the pharmacometabolomics study of OLZ. Statistical analysis revealed that tryptophan, 5-hydroxytryptophan, 5-hydroxytryptamine, γ-aminobutyric acid etc. were significantly downregulated, while tyrosine was significantly upregulated, which suggested that OLZ could promote the downstream phase II reaction of 5-hydroxytryptamine, inhibit tyrosine hydroxylase activity, and increase the activity of γ-aminobutyric acid transaminase. In conclusion, this method could provide novel insights for revealing the pharmacodynamic effect and mechanism of antipsychotic drugs.
  10. Chemosphere. 2022 Apr 30. pii: S0045-6535(22)01271-1. [Epub ahead of print] 134778
      β-Adrenergic agonist compounds are medicines that open up the lung's medium and large airways. β-Adrenergic agonist compounds have been illegally or legally used to increase lean muscle mass in meat animals, bodybuilding, weight-loss programs, and athletes. Developing a rapid analytical approach for determining β-adrenergic agonist compounds in biological samples is crucial for individual exposure assessment. This study established an analytical method for simultaneously measuring eight β-adrenergic agonist compounds in human urine, including clenbuterol, terbutaline, salbutamol, ractopamine, zilpaterol, cimaterol, tulobuterol, and fenoterol. Two hundred microliters of a urine sample were added to eight deuterium-labeled internal standard mixtures and glucuronidase/arylsulfatase for enzymatic hydrolysis, and were then analyzed using an online clean-up system coupled with a liquid chromatography-tandem mass spectrometry system (LC-MS/MS). The limit of quantification ranged from 0.03 to 0.12 ng/mL urine for the eight β-adrenergic agonist compounds. The relative standard deviations (RSD) of the within-run and between-run precisions were less than 10%, and the relative accuracy errors were less than 17% in the three-level spiked artificial urine samples. Two hundred eighty human urine samples collected from the general population in Taiwan were assessed to demonstrate the capability and feasibility of this method. The detection frequencies were 33% for clenbuterol, 5% for ractopamine, and less than 5% for the others. We concluded that the isotope dilution-online clean-up system coupled with LC-MS/MS method is a valuable analytical method for investigating urinary β-adrenergic agonist compounds in humans and is valuable for human biomonitoring studies.
    Keywords:  Biomonitoring; Human; Online SPE; Ractopamine; Urine; β-Adrenergic agonist
  11. J Pharm Biomed Anal. 2022 Apr 18. pii: S0731-7085(22)00196-0. [Epub ahead of print]216 114775
      For people with habits of chewing betel nuts and smoking, the probability of suffering from oral cancer is ten to a hundred times higher than others. Due to the serious health consequences of areca nut and tobacco, a reliable cessation program is needed. Hair is the best option to document long-term exposure. Unfortunately, the research on betel nut in hair did not attract much attention. In this study, a high-throughput method based on microwave-assisted extraction (MAE) and isotope dilution liquid chromatography tandem mass spectrometry (LC-MS/MS) was developed to measure the four biomarkers of betel nuts and cigarettes, including areca alkaloids (arecoline), tobacco alkaloids (nicotine), and their metabolites (arecaidine and cotinine). The hair sample was washed, cut, weighed, and incubated for 3 min MAE with methanol/trifluoroacetic acid, then evaporated and reconstituted for LC-MS/MS analysis. The total experiment time was 50 min. The lower limits of quantification (LOQ) were 5-10 pg/mg. The intra-day and inter-day precision were 2.2-7.6%. Intra-day and inter-day accuracy were - 6.1-8.2%. The method showed good linearity (r2 > 0.995) over LOQ - 1000 pg/mg concentration ranges. It was successfully applied to analyze 11 subjects of regular areca nut chewers, also smokers. Eight samples were black hair; three samples were naturally black hair with partially gray hair. Measured concentrations in black hair were in the range 56.9 pg/mg to 3.2 ng/mg for arecoline, 12.8 pg/mg to 222.2 pg/mg for arecaidine, 3.8 ng/mg to 33.4 ng/mg for nicotine and 1.1 ng/mg to 6.1 ng/mg for cotinine. The results showed lower levels in gray hair. This method was utilized successfully to analyze pg/mg levels of arecoline, arecaidine, nicotine, and cotinine, and good recoveries were obtained. The mean concentration of arecaidine and cotinine in hair was 15% and 20% of arecoline and nicotine, respectively. A good positive correlation was found between the concentrations of these compounds and self-report. This method improved extraction speed, concentration, and analysis of samples and is useful for monitoring betel nut and smoking cessation programs.
    Keywords:  Areca alkaloids; Hair; LC-MS/MS; Tobacco alkaloids
  12. J Chromatogr A. 2022 Apr 25. pii: S0021-9673(22)00281-3. [Epub ahead of print]1673 463088
      Many pharmacologically active compounds are chiral species, and their therapeutic or toxicological effects might differ between isomers. Herein, we develop a fast and sensitive chiral analysis methodology for the determination of eight pharmaceuticals, considered as emerging environmental pollutants and belonging to two different chemical classes, in wastewater and sludge samples. Compounds were separated using supercritical fluid chromatography (SFC) combined with time-of-flight mass spectrometry (TOF-MS) detection. The stationary phase, the modifier and the additive combined with supercritical carbon dioxide (CO2), in the SFC mobile phase, played a major effect in the enantiomeric resolution of selected compounds. Moreover, the composition of the mobile phase affected their ionization efficiency in the electrospray ionization source. Methanol (MeOH), containing a 0.1% of ammonia, was used as CO2 modifier for the separation of compounds in a polysaccharide-type column. Total analysis time was 15.5 min, achieving resolution factors between 1.03 and 2.49 for the eight pairs of enantiomers. In combination with mixed-mode solid-phase extraction and matrix solid-phase dispersion protocols, compounds were determined in wastewater and sludge samples, with limits of quantification in the range of 0.010-0.020 µg L-1 and 3.7-11.1 ng g-1, for aqueous and solid samples, respectively. The amine-type drugs (tramadol, propranolol and venlafaxine) were mostly found in wastewater samples, whilst azolic antimycotics were mainly quantified in sludge. The first group of compounds showed enantiomeric fractions significantly different to those existing in the commercial counterpart pharmaceuticals.
    Keywords:  Basic pharmaceuticals; Chiral separations; Mass spectrometry; Sludge; Supercritical fluid chromatography; Wastewater
  13. RSC Adv. 2021 Oct 18. 11(54): 33916-33925
      Prostate cancer is initially treated via androgen deprivation therapy (ADT), a highly successful treatment in the initial pursuit of tumour regression, but commonly restricted by the eventual emergence of a more lethal 'castrate resistant' (CRPC) form of the disease. Intracrine pathways that utilize dehydroepiandrosterone (DHEA) or other circulatory precursor steroids are thought to generate relevant levels of growth-stimulating androgens such as testosterone (T) and dihydrotestosterone (DHT). Decoding this tissue-specific metabolic pathway is key for the development of novel therapeutic treatments. Mass spectrometry imaging (MSI) is an analytical technique that allows the visualization of the distribution of numerous classes of biomolecules within tissue sections. The analysis of androgens by liquid chromatography mass spectrometry (LC/MS)-based methods however presents a challenge due to their generally poor ionization efficiency and low physiological endogenous levels. In MSI, on-tissue chemical derivatization (OTCD) has enabled the limits of steroids to be imaged within tissues to be pushed by overcoming poor ionization performance. However, isobaric interference of key androgen derivatives such as T and DHEA can severely hamper studying the intracrinology in several diseases. Here, we have evaluated the use of laser induced post-ionization (MALDI-2) combined with trapped ion mobility separation (TIMS) and orthogonal time-of-flight (QTOF) MS for the visualization of isobaric derivatized androgens in murine tumour xenograft at about 50 μm spatial resolution. With this combination, isobaric T and DHEA were separated in tissue sections and the signals of derivatized steroids enhanced by about 20 times. The combination of TIMS and MALDI-2 thus shows unique potential to study tissue intracrinology within target tissues. This could offer the opportunity for many novel insights into tissue-specific androgen biology.
  14. STAR Protoc. 2022 Jun 17. 3(2): 101311
      Metabolites are crucial for bidirectional communication between host and microbiome. We describe a protocol for the isolation of organic and aqueous metabolites from mucosal scrapes and feces from mouse and human samples. Although some of the most reactive organic compounds may be lost, this approach generates a functionally reproducible metabolic extract containing both host and microbial compounds appropriate for quantitative mass spectrometry and functional characterization. Our mass spectrometry approach identifies low-abundant and difficult to identify microbially derived metabolites. For complete details on the use and execution of this protocol, please refer to Bell et al. (2021) and Das et al. (2020).
    Keywords:  Mass Spectrometry; Metabolism; Metabolomics; Microbiology; Molecular Biology
  15. J Pharm Biomed Anal. 2022 Apr 08. pii: S0731-7085(22)00183-2. [Epub ahead of print]215 114762
      The targeted analysis of free fatty acids (FFAs) is attracting interest since several years with a plenty of studies. However, most of them are devoted to the solely determination of the short-chain fatty acids (SCFAs) arising from the symbiotic gut microbiota metabolism. Recently, the FFAs analysis highlighted changes in the plasma levels of octanoic and decanoic acids (medium-chain fatty acids or MCFAs) may be associated to gastrointestinal diseases, including colorectal cancer (CRC). Then, the simultaneous quantification of both SCFAs and MCFAs could be useful to put in evidence the interconnection between microbiota and metabolic alterations during hosts' disease. To this aim, it was developed an isotopic dilution gas-chromatography coupled mass spectrometry (ID/GC-MS) method for the targeted analysis of both linear and branched FFAs (SCFAs, MCFAs, and LCFAs) in human plasma samples as specific markers for both microbiota and host metabolic alterations. In order to minimize sample manipulation procedures, an efficient, sensible and low time-consuming procedure is presented, which relies in a simple liquid-liquid extraction before the determination of underivatized free acids (FFAs) by Single Ion Monitoring (SIM) acquisition. The reached detection limits (LODs) were less than 100 μg L-1 for most of analytes, except for acetic, hexadecanoic and octadecanoic acids that showed a LOD > 1 mg L-1. Methods accuracy and precision, obtained by the analysis of the FFAs mixtures showed accuracy values between 84% and 100% and precision (RSD %) between 0.1% and 12.4% at the concentration levels tested. The proposed ID/GC-MS method was applied in a case study to evaluate the FFAs as specific markers for both microbiota and host alterations in CRC patients. Obtained results highlight the advantage of present method for its rapidity, simplicity, and robustness.
    Keywords:  Colorectal cancer; Free fatty acids (FFA); ID/GC-MS; MCFA; SCFA