bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2022‒11‒06
sixteen papers selected by
Sofia Costa

  1. Nat Commun. 2022 Nov 04. 13(1): 6656
      Liquid chromatography - mass spectrometry (LC-MS) based untargeted metabolomics allows to measure both known and unknown metabolites in the metabolome. However, unknown metabolite annotation is a major challenge in untargeted metabolomics. Here, we develop an approach, namely, knowledge-guided multi-layer network (KGMN), to enable global metabolite annotation from knowns to unknowns in untargeted metabolomics. The KGMN approach integrates three-layer networks, including knowledge-based metabolic reaction network, knowledge-guided MS/MS similarity network, and global peak correlation network. To demonstrate the principle, we apply KGMN in an in vitro enzymatic reaction system and different biological samples, with ~100-300 putative unknowns annotated in each data set. Among them, >80% unknown metabolites are corroborated with in silico MS/MS tools. Finally, we validate 5 metabolites that are absent in common MS/MS libraries through repository mining and synthesis of chemical standards. Together, the KGMN approach enables efficient unknown annotations, and substantially advances the discovery of recurrent unknown metabolites for common biological samples from model organisms, towards deciphering dark matter in untargeted metabolomics.
  2. Int J Biol Markers. 2022 Oct 31. 3936155221132291
      INTRODUCTION: In this paper, an analytical pipeline designed for untargeted lipidomic profiling in human plasma is proposed. The analytical pipeline was developed for case-control studies nested in prospective cohorts.METHODS: The procedure consisted of isopropanol protein precipitation followed by reverse phase liquid chromatography coupled to high resolution mass spectrometry and software-assisted data processing. The compounds are putatively annotated by matching experimental mass spectrometry data with spectral library data using LipidSearch software. The lipid profile of a pool of plasma samples from 10 healthy volunteers was detected in both positive and negative polarity modes. The impact of the chosen polarity on the number and quality of the lipid identification has been evaluated.
    RESULTS: More than 1000 lipids from 12 different classes were detected, 1150 in positive mode and 273 in negative mode. Nearly half of them were unambiguously identified by the software in positive mode, and about one-third in negative mode. The method repeatability was assessed on the plasma pool samples by means of variance components analysis. The intra- and inter-assay precision was measured for 10 lipids chosen among the most abundant found within the different lipid classes. The intra-assay coefficients of variation ranged from 2.56% to 4.56% while intra- and inter-day coefficients of variance never exceeded the 15% benchmark adopted. The lipidomic profiles of the 10 healthy volunteers were also investigated.
    DISCUSSION: This method detects a wide range of lipids and reports their degree of identification. It is particularly fit and well-designed for large case-control epidemiologic studies.
    Keywords:  Clinical and molecular epidemiology; epidemiology; mass spectrometry methods; metabolomics methods
  3. Gigascience. 2022 Nov 03. pii: giac101. [Epub ahead of print]11
      BACKGROUND: Reproducibility of liquid chromatography separation is limited by retention time drift. As a result, measured signals lack correspondence over replicates of the liquid chromatography-mass spectrometry (LC-MS) experiments. Correction of these errors is named retention time alignment and needs to be performed before further quantitative analysis. Despite the availability of numerous alignment algorithms, their accuracy is limited (e.g., for retention time drift that swaps analytes' elution order).RESULTS: We present the Alignstein, an algorithm for LC-MS retention time alignment. It correctly finds correspondence even for swapped signals. To achieve this, we implemented the generalization of the Wasserstein distance to compare multidimensional features without any reduction of the information or dimension of the analyzed data. Moreover, Alignstein by design requires neither a reference sample nor prior signal identification. We validate the algorithm on publicly available benchmark datasets obtaining competitive results. Finally, we show that it can detect the information contained in the tandem mass spectrum by the spatial properties of chromatograms.
    CONCLUSIONS: We show that the use of optimal transport effectively overcomes the limitations of existing algorithms for statistical analysis of mass spectrometry datasets. The algorithm's source code is available at
    Keywords:  Wasserstein distance; liquid chromatography–mass spectrometry; retention time alignment; simplex algorithm
  4. Rapid Commun Mass Spectrom. 2022 Nov 02. e9427
      RATIONALE: Exosomes contain biomarkers such as proteins and lipids that help in understanding normal physiology and diseases. Lipids, in particular, are infrequently studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) for biomarker discovery. In this study, MALDI was equipped with a high-resolution MS to investigate the exosomal lipid from human serum.METHODS: Exosomal lipids were profiled by MALDI with Fourier-transform ion cyclotron resonance mass spectrometry (FTICR MS). Four matrices, i.e., α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (DHB), sinapinic acid (SA), and graphene oxide (GO), along with three sample preparation methods, i.e., dried droplet, thin-layer, and two-layer, were compared in terms of the number of lipid species detected and the relative abundance of each lipid from human serum and human serum exosomes.
    RESULTS: In total, 172 and 89 lipid species were identified from human serum and human serum exosomes, respectively, by all of the methods used. The greatest number of exosome lipid species, 69, was detected with the CHCA matrix, while only 8 exosome lipid species were identified with the GO matrix. Among the identified lipid species, phosphatidylcholine was identified most frequently, probably due to the use of a positive ion mode.
    CONCLUSIONS: Exosomes and human serum showed comparable lipid profiles as determined by MALDI-FTICR MS. These findings provide a new perspective on exosomal lipidomics analysis and may serve as a foundation for future lipidomics-based biomarker research using MALDI-FTICR MS.
  5. J Chromatogr A. 2022 Oct 23. pii: S0021-9673(22)00789-0. [Epub ahead of print]1685 463598
      Characterization of complex lignin degradation products by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) requires a high sensitivity, which can be improved by use of optimized mobile phase additive. In this study, chromatographic separation and ionization efficiency for LC-MS analysis of lignin oligomers and lignin-derived phenolic compounds were compared among six different mobile phase additives. We found that acetic acid exhibits analytical performance superior to the other mobile phase additives for characterization of lignin degradation products by LC-(-)-ESI-MS/MS. The retention of phenolic compounds (PCs) containing carboxylic group was improved by using acidic additives instead of their ammonium salts. The use of acetic acid as an LC mobile phase additive enhanced the ionization efficiency of PCs in (-)-ESI-MS about 2 to 4 times higher than the other additives. The improved MS sensitivity with acetic acid yielded a higher coverage of fragment ions in LC-MS/MS analysis, leading to identification of four additional synthetic G-type lignin oligomers (LOs) than ammonium acetate. A similar degree of sensitivity enhancement was also demonstrated for degradation products from rice straw lignin using acetic acid additive over the others. The increased chromatographic retention and enhanced sensitivity of PCs and LOs provided by the use of acetic acid as an LC-(-)-ESI-MS mobile phase additive will facilitate structural analysis of lignin degradation products without relying on additional instrumentation.
    Keywords:  Electrospray ionization mass spectrometry; Lignin degradation product; Lignin oligomer; Mobile phase additive; Phenolic compound
  6. Clin Nutr. 2022 Oct 13. pii: S0261-5614(22)00357-0. [Epub ahead of print]41(12): 2637-2643
      BACKGROUND: Some fatty acids, i.e. n-3 and n-6 polyunsaturated fatty acids (PUFA), from metabolomics platforms based on nuclear magnetic resonance imaging (NMR) or liquid chromatography mass-spectrometry (LC-MS) are suggested to reflect dietary exposure. NMR and LC-MS are both relatively fast and cheap, however few studies have investigated their validity. Linoleic acid (LA) and docosahexaenoic acid (DHA), measured using gas chromatography (GC), are established biomarkers of dietary n-6 and n-3 PUFA intake, respectively.OBJECTIVE: To examine if circulating fatty acids derived from two commonly applied metabolomics platforms (using NMR and LC-MS) provide similar information compared to GC in two pooled population-based cohorts, one patient cohort, and in a randomized controlled trial (RCT).
    METHODS: Spearman rank correlations were conducted between LA and DHA in cholesteryl esters (CE) from GC and whole serum/plasma LA and DHA from the metabolomics platforms in a pooled population-based cohort of men and women (n ˜ 1100) (primary analysis). Secondary correlation analyses included fatty acid classes such as n-3 PUFA, n-6 PUFA, saturated fatty acids (SFA), monounsaturated fatty acids (MUFA) and total PUFA. Additionally, correlations were investigated for LA, DHA and the five fatty acid classes in phospholipids (PL), triacylglycerols (TAG) and non-esterified fatty acids (NEFA) in a RCT of n = 60 as well as in a population with biopsy-verified non-alcoholic fatty liver disease (NAFLD) (n = 59). Misclassification was examined using cross-tabulation and visualized using alluvial plots.
    RESULTS: Moderate to strong correlations (r = 0.51-0.81) were observed for LA and DHA in multiple lipid fractions in all cohorts using the NMR platform. For the pooled cohort, LA (r = 0.67, P < 0.0001) and DHA (r = 0.68, P < 0.0001) assessed in CE were strongly correlated with LA and DHA derived using NMR. Nearly half (49%) were correctly classified into their respective quartiles. Using LC-MS, only DHA (r = 0.44, P < 0.0001) demonstrated moderate correlations with DHA from GC.
    CONCLUSIONS: Unless fatty acid data from GC analysis is available or feasible, NMR-based technology might be a better option than a LC-MS-based platform, at least for certain PUFA. This should be taken into account in future studies aiming to use circulating fatty acids as dietary biomarkers for the investigation of diet-disease relationships.
    Keywords:  Epidemiology; Fatty acids; Metabolomics; Nutrition; Validation
  7. Anal Bioanal Chem. 2022 Nov 01.
      Large-scale lipidomic analyses have been limited by the cost and accessibility of traditional venipuncture sampling. Microsampling techniques offer a less-invasive and more accessible alternative. From a single drop of blood, plasma separation cards (PSC) deliver two volumetric dried plasma samples which are studied here for profiling endogenous blood lipids. Six lots of EDTA-treated human whole blood were used to compare PSC, dried blood spot analyses (DBS), and classic wet plasma extractions. Six replicate extractions were performed for each lot. Nontargeted lipidomics was performed by liquid chromatography-high resolution tandem mass spectrometry. Lipids were annotated by accurate mass/retention time matching and MS/MS spectral library matching using peak intensities for quantitation. Four hundred ninety-eight compounds covering 24 lipid subclasses were annotated. Inter-lot repeatability was evaluated by the percent relative standard deviation (%RSD) for each lot, giving median %RSD values across the lots at 14.6% for PSC, 9.3% for DBS, and 8.6% for wet plasma. Strong correlations of lipid peak intensities between wet plasma and PSCs were observed, but less for DBS. Lipid recovery and stability were comparable between the PSC and DBS samples, with roughly 60% of annotated lipids stable at room temperature after 28 days. Overall, PSCs provide a better alternative for quantitative blood lipidomic analyses compared to dried blood spots. However, problems with lipid stability for samples handled and shipped at room temperature are currently unavoidable outside of a clinical setting. Data transferability and comparability to standard plasma is lipid and lipid class dependent.
    Keywords:  Lipidomics; Mass spectrometry; Method validation; Microsampling
  8. J Chromatogr A. 2022 Oct 14. pii: S0021-9673(22)00753-1. [Epub ahead of print]1685 463562
      A direct injection liquid chromatography-tandem mass spectrometry method was successfully developed for the analysis of 19 illicit drugs and psychopharmaceuticals in raw and treated wastewater. The method includes the analysis of stimulants and opioids, and antidepressant, antipsychotic, antianxiety, appetite suppressant and hallucinogen drugs. The method limits of quantification range from 5 - 59 ng L-1 and 2 - 38 ng L-1 in raw and treated wastewater, respectively. Analysis of raw and treated wastewater samples collected daily for a week from a wastewater treatment plant operating with oxidation ditch technology showed that codeine and tramadol were the drugs with the highest median mass concentrations in raw wastewater (1800 and 1000 ng L-1, respectively). The presence of some of the drugs in treated wastewater samples implies incomplete removal of illicit drugs and psychopharmaceuticals during wastewater treatment. This method offers an alternative to existing methods for faster screening of wastewater samples without the need for sample pre-concentration techniques, such as solid-phase extraction, with limits of detection in the low nanogram per litre range.
    Keywords:  Direct injection; Illicit drugs; Liquid chromatography-tandem mass spectrometry; Psychopharmaceuticals; Wastewater
  9. Food Technol Biotechnol. 2022 Sep;60(3): 406-417
      Research background: Considering the importance of consumption of berry fruits with proven health-beneficial properties and difficulties in quality control of products of specific botanical and geographic origin, a fingerprint method was developed, based on advanced data analysis (pattern recognition, classification), in order to relate the variability of nutrients in the selected cultivars to primary metabolite profile.Experimental approach: Forty-five samples of genuine berry fruit cultivars (strawberry, raspberry, blackberry, black currant, blueberry, gooseberry, chokeberry, cape gooseberry and goji berry) were characterized according to chromatographic profiles of primary metabolites (sugars, lipids and fatty acids) obtained by three chromatographic techniques (high-performance thin-layer chromatography, gas chromatography coupled to mass spectrometry, and high-performance anion-exchange chromatography with pulsed amperometric detection).
    Results and conclusions: Comprehensive analysis allowed monitoring and identification of metabolites belonging to polar lipids, mono-, di- and triacylglycerols, free fatty acids, free sterols, sterol esters, mono- to heptasaccharides and sugar alcohols. Chemical fingerprint of berry seeds showed the uniformity of primary metabolites within each fruit species, but revealed differences depending on the botanical origin. All three chromatographic methods provided a discriminative, informative and predictive metabolomics methodology, which proved to be useful for chemotaxonomic classification.
    Novelty and scientific contribution: A novel methodology for the identification of bioactive compounds from primary metabolites of natural products was described. The proposed untargeted metabolite profiling approach could be used in the future as a routine method for tracing of novel bioactive compounds. The knowledge of metabolite composition obtained in this study can provide a better assessment of genotypic and phenotypic differences between berry fruit species and varieties, and could contribute to the development of new breeding programs.
    Keywords:  berry seeds; chemical fingerprint; chromatography techniques; sugar, lipid and fatty acid identification
  10. Anal Chem. 2022 Nov 03.
      Substrate-based electrospray ionization (ESI) techniques like paper, wooden tip, plastic tip, and metal-needle-based spray suffer from corona discharge, high background noise, and unstable spray in negative ionization mode, especially for the analysis of complex biological matrices, such as blood and urine. Coated blade spray coupled with mass spectrometry (CBS-MS) combines solid-phase microextraction's (SPME) efficient sample clean-up and enrichment and ambient MS's fast analysis and has proven to be an appealing alternative tool for the fast screening of target analytes in complex matrices. This paper documents the development of a new CBS blade design that features a barrier at the far end of the ESI tip. The findings of this work show that the addition of this simple barrier enabled the total RSD% to be reduced to less than 10% for sample preparation, ionization, and the MS detection of several drugs of abuse in negative mode, without compensation using internal standards. The improved stability of ESI in negative mode was investigated by observing the ESI process with a microscope camera and testing via CBS-MS. The new design was applied for the analysis of three drugs of abuse in urine, with the calibration curve correlation coefficient (R2 ≥ 0.9997) being calculated without the use of internal standards. The overall RSD% of the peak area for one compound in 42 samples was 6.9%, which highlights the method's incredible reproducibility compared to other ambient MS techniques for analyzing real samples. The CBS device with a barrier was also applied for the on-blade sampling of 14 drugs of abuse in 20 μL of plasma spot in positive ionization mode. The results of these tests yielded a calibration curve correlation coefficient of R2 ≥ 0.9883 and limits of quantification (LOQs) between 0.25 and 25 ng/mL. The obtained results provide guidance on CBS device design optimization and the effective automation of the protocol.
  11. Handb Exp Pharmacol. 2022 Nov 02.
      Natural products have been the most important source for drug development throughout the human history. Over time, the formulation of drugs has evolved from crude drugs to refined chemicals. In modern drug discovery, conventional natural products lead-finding usually uses a top-down approach, namely bio-guided fractionation. In this approach, the crude extracts are separated by chromatography and resulting fractions are tested for activity. Subsequently, active fractions are further refined until a single active compound is obtained. However, this is a painstakingly slow and expensive process. Among the alternatives that have been developed to improve this situation, metabolomics has proved to yield interesting results having been applied successfully to drug discovery in the last two decades. The metabolomics-based approach in lead-finding comprises two steps: (1) in-depth chemical profiling of target samples, e.g. plant extracts, and bioactivity assessment, (2) correlation of the chemical and biological data by chemometrics. In the first step of this approach, the target samples are chemically profiled in an untargeted manner to detect as many compounds as possible. So far, NMR spectroscopy, LC-MS, GC-MS, and MS/MS spectrometry are the most common profiling tools. The profile data are correlated with the biological activity with the help of various chemometric methods such as multivariate data analysis. This in-silico analysis has a high potential to replace or complement conventional on-silica bioassay-guided fractionation as it will greatly reduce the number of bioassays, and thus time and costs. Moreover, it may reveal synergistic mechanisms, when present, something for which the classical top-down approach is clearly not suited. This chapter aims to give an overview of successful approaches based on the application of chemical profiling with chemometrics in natural products drug discovery.
    Keywords:  Antibiotics; Chemometrics; Correlation analysis; Discriminant analysis; In-silico; Metabolomics; anti-inflammatory; anticancer
  12. Crit Rev Anal Chem. 2022 Nov 03. 1-8
      Although as an analytical method with high specificity and high sensitivity, mass spectrometry (MS) has a wide range of applications in many fields, it still needs other technologies as the assist and supplement to enhance the scope and capability of analysis. Coupling with ion mobility (IM) can make an enhancement effect in the field of pharmaceutical analysis as a supplementary method. The two-dimensional mass technology improves the confidence of compounds annotations while increasing peak capacity, with the gradual deepening of theoretical research on IM-MS, it has shown unique advantages in the complex analysis conditions. IM-MS owns great potential for improving the depth, range, dimension of in-depth drug research. In this review, the principle, instruments and methods, applications, advantages and limitations of IM-MS are described. Here, we also elaborate on the prospects in structural evaluation, separation, and identification of complex compounds for the drug discovery and development phase and the great advantages of macromolecules and omics.
    Keywords:  Applications; complex compounds; ion mobility-mass spectrometry; macromolecules; omics
  13. Rapid Commun Mass Spectrom. 2022 Nov 03. e9425
      RATIONALE: Tuberculosis remains a challenging global infectious disease, mainly affecting the lungs. First-line antituberculosis drugs play a crucial role in slowing down the rapid spread of tuberculosis. In addition, the patient might benefit from therapeutic drug monitoring since it has become an accepted clinical tool for optimizing tuberculosis treatment.METHODS: A simple and sensitive liquid chromatography/tandem mass spectrometry method was developed to monitor the plasma level of isoniazid, ethambutol and pyrazinamide in plasma samples. A one-step extraction procedure using an OSTROTM plate was applied, and extracts were analyzed by gradient elution followed by detection on a mass spectrometer by multiple reaction monitoring mode.
    RESULTS: The analytes were separated within 4.2 min and over the concentration range of 0.2-10 μg/mL for isoniazid and ethambutol and 1-65 μg/mL for pyrazinamide. The method was successfully validated according to the European Medicine Agency guideline for the selectivity, linearity and lower limit of detection, precision and accuracy, matrix effect, extraction recovery, carryover, dilution integrity and stability and applied for quantification of analytes in clinical samples from tuberculosis patients.
    CONCLUSIONS: The presented method allows sensitive and reproducible determination of selected antituberculosis drugs with an advantage such as low sample volume requirement, a short run time of analysis, a one-step sample preparation procedure with capabilities for phospholipids removal, and a low quantification limit as well as a high degree of selectivity.
  14. Chem Pharm Bull (Tokyo). 2022 ;70(11): 796-804
      We have developed a simple and accurate method for quantifying sugars in herbal medicines, which have hitherto been difficult to quantify. Using ultra performance liquid chromatography-quadrupole-time-of-flight (UPLC-Q-TOF)-MS and two types of columns with different chemical properties, we determined the optimum conditions for separating nine sugars (fructose, galactose, glucose, mannitol, sucrose, melibiose, raffinose, manninotriose, and stachyose) commonly found in herbal medicines. Separation was completed within 10 min when an apHera NH2 HPLC column was used, although galactose and glucose could not be separated. On the other hand, the nine sugars were completely separated within 16 min when a hydrophilic interaction chromatography (HILIC)pak VG-50 2D column was used. The calibration curves obtained using those two columns gave good linearity for the sugar standards, and the coefficient of determination was 0.995 or higher. Both columns showed excellent performance with short analysis time and high sensitivity. Using our developed method, we were able to quantify sugars in galactose-free herbal medicines within 10 min and in herbal medicines containing galactose within 16 min. We revealed that our method could be used for the analysis of sugars in Angelica acutiloba and Rehmannia glutinosa roots.
    Keywords:  herbal medicine; quality evaluation; simple method; sugar quantification; ultra performance liquid chromatography (UPLC)/MS
  15. Electrophoresis. 2022 Nov 03.
      Capillary electrophoresis (CE) is a powerful separation tool for non-targeted analysis of chemically complex samples, such as blood, urine, and tissue. However, traditionally CE requires samples in solution for analysis, which limits information on analyte distribution and heterogeneity in tissue. The recent development of surface sampling capillary electrophoresis mass spectrometry (SS-CE-MS) brings these advantages of CE to solid samples and enables chemical mapping directly from the tissue surface without any molecular preselection or sample preparation. This opens new possibilities to understand the chemistry in complex solid samples such as tissue sections, where distinct morphological regions can be targeted, as well as uniform samples such as blood spots. Here, we describe developments of SS-CE-MS to increase reproducibility, stability, and throughput. With the addition of a sheath liquid and optimized conditions we report extraction and separation of metabolites, lipids and proteins from rat brain tissue section and dried blood spots. Additionally, we report the first electrokinetic sequential sample injection for high throughput analysis. We foresee that the wide molecular coverage from a distinct tissue region in combination with higher throughput will provide novel information on biological function and dysfunction. This article is protected by copyright. All rights reserved.
    Keywords:  capillary electrophoresis-mass spectrometry; dried blood spots; omics; surface sampling; tissue sections
  16. Shokuhin Eiseigaku Zasshi. 2022 ;63(5): 177-181
      A liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based method was developed for determining quinclorac in livestock products. Quinclorac was extracted from the samples using a solution of acetone and hydrochloric acid mixed in a 99 : 1 ratio. The crude extract was purified with ethyl acetate under basic conditions, followed by quinclorac extraction with ethyl acetate under acidic conditions and analysis using LC-MS/MS. The average recoveries of quinclorac from five livestock products (n=5) fortified at the maximum residue limits or 0.01 mg/kg ranged from 85.6 to 93.5%, with the precision of repeatability ranging from 1.7 to 6.8%. The quantification limit in this analytical method was 0.01 mg/kg. These results suggest that the developed method is useful for analyzing quinclorac in livestock products.
    Keywords:  LC-MS/MS; herbicide; livestock products; quinclorac