bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2021‒02‒21
thirteen papers selected by
Sofia Costa
Cold Spring Harbor Laboratory


  1. J Chromatogr A. 2021 Jan 23. pii: S0021-9673(21)00057-1. [Epub ahead of print]1640 461933
    Faqehi AM, Denham SG, Naredo G, Cobice DF, Khan S, Simpson JP, Sabil G, Upreti R, Gibb F, Homer NZ, Andrew R.
      Liquid Chromatography tandem mass spectrometry (LC-MS/MS) is the gold-standard approach for androgen analysis in biological fluids, superseding immunoassays in selectivity, particularly at low concentrations. While LC-MS/MS is established for analysis of testosterone and androstenedione, 5α-dihydrotestosterone (DHT) presents greater analytical challenges. DHT circulates at low nanomolar concentrations in men and lower in women, ionizing inefficiently and suffering from isobaric interference from other androgens. Even using current LC-MS/MS technology, large plasma volumes (>0.5 mL) are required for detection, undesirable clinically and unsuitable for animals. This study investigated derivatization approaches using hydrazine-based reagents to enhance ionization efficiency and sensitivity of analysis of DHT by LC-MS/MS. Derivatization of DHT using 2-hydrazino-1-methylpyridine (HMP) and 2-hydrazino-4-(trifluoromethyl)-pyrimidine (HTP) were compared. A method was validated using an UHPLC interfaced by electrospray with a triple quadruple mass spectrometer , analyzing human plasma (male and post-menopausal women) following solid-phase extraction. HMP derivatives were selected for validation affording greater sensitivity than those formed with HTP. HMP derivatives were detected by selected reaction monitoring (DHT-HMP m/z 396→108; testosterone-HMP m/z 394→108; androstenedione-HMP m/z 392→108). Chromatographic separation of androgen derivatives was optimized, carefully separating isobaric interferents and acceptable outputs for precision and trueness achieved following injection of 0.4 pg on column (approximately 34 pmol/L). HMP derivatives of all androgens tested could be detected in low plasma volumes: male (100 µL) and post-menopausal female (200 µL), and derivatives were stable over 30 days at -20°C. In conclusion, HMP derivatization, in conjunction with LC-MS/MS, is suitable for quantitative analysis of DHT, testosterone and androstenedione in low plasma volumes, offering advantages in sensitivity over current methodologies.
    Keywords:  5α-Dihydrotestosterone; Androstenedione; Derivatization; Liquid chromatography mass spectrometry; Testosterone
    DOI:  https://doi.org/10.1016/j.chroma.2021.461933
  2. J Agric Food Chem. 2021 Feb 19.
    Han X, Ye H.
      Triglyceride (TG) is a class of neutral lipids, which functions as an energy storage depot and is important for cellular growth, metabolism, and function. The composition and content of TG molecular species are crucial factors for nutritional aspects in food chemistry and are directly associated with several diseases, including atherosclerosis, diabetes, obesity, stroke, etc. As a result of the complexities of aliphatic moieties and their different connections/locations to the glycerol backbone in TG molecules, accurate identification of individual TG molecular species and quantitative assessment of TG composition and content are particularly challenging, even at the current stage of lipidomics development. Herein, methods developed for analysis of TG species, such as liquid chromatography-mass spectrometry with a variety of columns and different mass spectrometric techniques, shotgun lipidomics approaches, and ion-mobility-based analysis, are reviewed. Moreover, the potential limitations of the methods are discussed. It is our sincere hope that the overviews and discussions can provide some insights for researchers to select an appropriate approach for TG analysis and can serve as the basis for those who would like to establish a methodology for TG analysis or develop a new method when novel tools become available. Biologically accurate analysis of TG species with an enabling method should lead us toward improving the nutritional quality, revealing the effects of TG on diseases, and uncovering the underlying biochemical mechanisms related to these diseases.
    Keywords:  lipidomics; mass spectrometry; metabolic syndrome; regioisomers; shotgun lipidomics; triglycerides
    DOI:  https://doi.org/10.1021/acs.jafc.0c07175
  3. Anal Chim Acta. 2021 Mar 15. pii: S0003-2670(21)00050-7. [Epub ahead of print]1150 338224
    Shafaei A, Rees J, Christophersen CT, Devine A, Broadhurst D, Boyce MC.
      With rapid advances in gut microbiome research, fecal bile acids are increasingly being monitored as potential biomarkers of diet related disease susceptibility. As such, rapid, robust and reliable methods for their analysis are of increasing importance. Herein is described a simple extraction method for the analysis of bile acids in feces suitable for subsequent quantification by liquid chromatography and tandem mass spectrometry. A C18 column separated the analytes with excellent peak shape and retention time repeatability maintained across 800 injections. The intra-day and inter-day precision and accuracy was greater than 80%. Recoveries ranged from 83.58 to 122.41%. The limit of detection and limit of quantification were in the range 2.5-15 nM, respectively. The optimized method involved extracting bile acids from wet feces with minimal clean up. A second aliquot of fecal material was dried and weighed to correct for water content. Extracting from dried feces showed reduced recovery that could be corrected for by spiking the feces with deuterated standards prior to drying. Storage of the extracts and standards in a refrigerated autosampler prior to analysis on the LC-MS is necessary. Multiple freeze-thaws of both extracts and standards lead to poor recoveries for some bile acids. The method was successfully applied to 100 human fecal samples.
    Keywords:  Bile acids; Extraction; Fecal; LC-MS/MS; Stability
    DOI:  https://doi.org/10.1016/j.aca.2021.338224
  4. J Biosci Bioeng. 2021 Feb 13. pii: S1389-1723(20)30440-0. [Epub ahead of print]
    Hayashi Y, Komatsu T, Iwashita K, Fukusaki E.
      Six categories of Japanese sake have been established by the National Tax Agency of Japan. In this system, the rice polishing ratio and the addition of alcohol are the main criteria for classification. The most common nuclear magnetic resonance (NMR) spectrometry method is 1H-NMR, and has higher throughput than gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS) analysis due to its short measurement time, easy sample preparation, and high reproducibility. However, owing to the production of dominant ethanol signals, metabolome analyses have not been used for classifying Japanese sake using 1H-NMR. In this study, a technique to selectively suppress ethanol signals was used to classify Japanese sake by 1H-NMR, and a model was constructed to predict the rice polishing ratio. The results were compared to those obtained by GC-MS. The suppression of ethanol signals enabled the detection of trace components by 1H-NMR. In a principal component analysis (PCA) score plot of 1H-NMR spectra with ethanol signal suppression, PC1 was associated with both the addition of alcohol and the rice polishing ratio. Additionally, the separation of samples observed was similar when PCA score plots of 1H-NMR and GC-MS data were compared. Similarly, to predict the rice polishing ratio using partial least squares regression analysis, a model was constructed using 1H-NMR data, and showed nearly similar values for precision and predictive performance with the model constructed using GC-MS data. These results suggest that metabolomic analyses of Japanese sake based on 1H-NMR spectral patterns may be useful for classification.
    Keywords:  (1)H-nuclear magnetic resonance spectrometry; Classification; Gas chromatography–mass spectrometry; Japanese sake; Metabolomics
    DOI:  https://doi.org/10.1016/j.jbiosc.2020.12.008
  5. J Pharm Biomed Anal. 2021 Feb 02. pii: S0731-7085(21)00055-8. [Epub ahead of print]197 113943
    Kogaki T, Ohshio I, Ura H, Iyama S, Kitae K, Morie T, Fujii S, Sato S, Nagata T, Takeda AH, Aoki M, Ueda K, Minami K, Yamamoto M, Kawahara K, Furukawa T, Sato M, Ueda Y, Jingushi K, Tozuka Z, Saigusa D, Hase H, Tsujikawa K.
      There are more than 150 types of naturally occurring modified nucleosides, which are believed to be involved in various biological processes. Recently, an ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) technique has been developed to measure low levels of modified nucleosides. A comprehensive analysis of modified nucleosides will lead to a better understanding of intracellular ribonucleic acid modification, but this analysis requires high-sensitivity measurements. In this perspective, we established a highly sensitive and quantitative method using the newly developed ion source, UniSpray. A mass spectrometer was used with a UniSpray source in positive ion mode. Our UHPLC-UniSpray-MS/MS methodology separated and detected the four major nucleosides, 42 modified nucleosides, and dG15N5 (internal standard) in 15 min. The UniSpray method provided good correlation coefficients (>0.99) for all analyzed nucleosides, and a wide range of linearity for 35 of the 46 nucleosides. Additionally, the accuracy and precision values satisfied the criteria of <15% for higher concentrations and <20% for the lowest concentrations of all nucleosides. We also investigated whether this method could measure nucleosides in biological samples using mouse tissues and non-small cell lung cancer clinical specimens. We were able to detect 43 and 31 different modified nucleosides from mouse and clinical tissues, respectively. We also found significant differences in the levels of N6-methyl-N6-threonylcarbamoyladenosine (m6t6A), 1-methylinosine (m1I), 2'-O-methylcytidine (Cm), 5-carbamoylmethyluridine (ncm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5S2U), and 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) between cancerous and noncancerous tissues. In conclusion, we developed a highly sensitive methodology using UHPLC-UniSpray-MS/MS to simultaneously detect and quantify modified nucleosides, which can be used for analysis of biological samples.
    Keywords:  Modified nucleosides; Non-small cell lung cancer; Ribonucleic acid; UHPLC-MS/MS; UniSpray
    DOI:  https://doi.org/10.1016/j.jpba.2021.113943
  6. Anal Chim Acta. 2021 Mar 22. pii: S0003-2670(20)31238-1. [Epub ahead of print]1151 238170
    Wahab MF, Roy D, Armstrong DW.
      Modern high-throughput experimentation and challenging analytical problems of academic/industrial research have put the responsibility on separation scientists to develop new fast separation approaches. With the availability of high-pressure pumps, small particles with hydrolytically stable surface chemistries, reduced extra-column band broadening, and low volume detectors with fast signal processing, it is now feasible to do sub-minute to sub-second chromatography. Herein, the fundamental theoretical principles of ultrafast chromatography, along with practical solutions, are reviewed. Approaches for rapid separations in packed beds, narrow open tubular columns, and monoliths are demonstrated, along with the challenges that were faced. The instrumentation requirements (pumps, injection systems, detectors, column packing process) for using short columns ranging from 0.5 to 5 cm are examined, followed by real applications. One of the main problems in ultrafast chromatography is partial or complete peak overlap. As per Gidding's statistical overlap theory, peak overlap cannot be avoided for a completely random sample for a column with a given peak capacity. Signal processing techniques based on Fourier transform deconvolution of band broadening, power laws, derivatives, and iterative curve fitting are explained to help improve the chromatographic resolution. An example of ten peaks separated in under a second is shown and discussed. Other ultrafast separations in supercritical fluid chromatography or capillary electrophoresis are briefly mentioned to provide a complete understanding of this emerging field.
    Keywords:  Chiral separations; High-throughput liquid chromatography; Hydrophilic interaction liquid chromatography; Narrow open-tubular columns; Short columns; Signal processing; Sub-second separations
    DOI:  https://doi.org/10.1016/j.aca.2020.12.045
  7. J Pharm Biomed Anal. 2021 Jan 29. pii: S0731-7085(21)00040-6. [Epub ahead of print]196 113928
    Kahl JMM, da Cunha KF, Rodrigues LC, Chinaglia KO, Oliveira KD, Costa JL.
      The abuse of stimulants such as amphetamine, methamphetamine, ecstasy (MDMA), and their analogues (MDEA and MDA) has been increasing considerably worldwide since 2009. In this work, an analytical method using dispersive liquid-liquid microextraction (DLLME) to determine amphetamine and derivatives in oral fluid samples by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed and validated. Linearity was achieved between 20 to 5000 ng/mL (r>0.992, 1/x² weighted linear regression), with a limit of quantification (LOQ) of 20 ng/mL. Imprecision (%relative standard deviation) and bias (%) were not higher than 9.1 and -12.3%, respectively. The matrix effect was lower than 14.6%, with no carryover observed up to 5000 ng/mL and no interference with 10 different oral fluid matrix sources and against 14 pharmaceuticals and other common drugs of abuse. MDMA, MDA, and MDEA in processed samples were stable up to 24 h at autosampler (10°C); and amphetamine and methamphetamine up to 18 h. The developed method was successfully applied to authentic oral fluid analyses (n = 140). The proposed method is an example of the Green Analytical Toxicology, since it reduces both the amount of solvent required in samples preparation and the quantity of solvents and reagents used in analytical-instrumental stage, as well as requires a minimal sample volume, being a cheaper, quicker and more ecological alternative to conventional methods. Obtained results showed that DLLME extraction combined with LC-MS/MS is a fast and simple method to quantify amphetamine derivatives in oral fluid samples.
    Keywords:  Amphetamines; Dispersive liquid-liquid microextraction (DLLME); Forensic toxicology; Green analytical toxicology (GAT); MDMA; Oral fluid
    DOI:  https://doi.org/10.1016/j.jpba.2021.113928
  8. Anal Chem. 2021 Feb 14.
    La Rocca R, Kune C, Tiquet M, Stuart L, Eppe G, Alexandrov T, De Pauw E, Quinton L.
      Mass spectrometry imaging (MSI) is a powerful and convenient method for revealing the spatial chemical composition of different biological samples. Molecular annotation of the detected signals is only possible if a high mass accuracy is maintained over the entire image and the m/z range. However, the change in the number of ions from pixel-to-pixel of the biological samples could lead to small fluctuations in the detected m/z-values, called mass shift. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. Their "a priori" selection for a global MSI acquisition is prone to false positive detection and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of pixel-specific internal calibrating ions, automatically generated in a data-adaptive manner (https://github.com/LaRoccaRaphael/MSI_recalibration). Through a practical example, we applied the methodology to a zebrafish whole-body section acquired at a high mass resolution to demonstrate the impact of mass shift on data analysis and the capability of our algorithm to recalibrate MSI data. In addition, we illustrate the broad applicability of the method by recalibrating 31 different public MSI data sets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations (gaining from 20 up to 400 additional annotations), particularly the high-confidence annotations with a low false discovery rate.
    DOI:  https://doi.org/10.1021/acs.analchem.0c05071
  9. J Am Soc Mass Spectrom. 2020 Dec 02. 31(12): 2392-2400
    Palermo A.
      The study of metabolism heterogeneity is essential to understand the role of metabolites in supporting and regulating biological functions. To this end, several mass spectrometry imaging (MSI) approaches have been proposed for the detection of small molecule metabolites. However, high noise from the ionization matrix and low metabolome coverage hinder their applicability for untargeted metabolomics studies across space. In this context, nanostructure imaging (/initiator) mass spectrometry (NIMS) and NIMS with fluorinated gold nanoparticles (f-AuNPs) are attractive strategies for comprehensive MSI of metabolites in biological systems, which can provide heterogeneous metabolome coverage, ultrahigh sensitivity, and high lateral resolution. In particular, NIMS with f-AuNPs permits the simultaneous detection of polar metabolites and lipids in a single and cohesive analytical session, thus allowing the systems-level interpretation of metabolic changes. In this Perspective article, we discuss the use of NIMS and f-AuNPs in the exploration of metabolism heterogeneity and provide a critical outlook on future applications of this technology for revealing the metabolic architecture that supports biological functions in health and disease, from whole organisms to tissues, single cells, and subcellular compartments.
    Keywords:  Nanostructure imaging mass spectrometry; metabolism heterogeneity; metabolomics; single cell approaches; subcellular metabolism; systems biology
    DOI:  https://doi.org/10.1021/jasms.0c00204
  10. Rapid Commun Mass Spectrom. 2021 Feb 16. e9068
    Thompson AM, Stratton KG, Bramer LM, Zavoshy NS, McCue LA.
      RATIONALE: Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a preferred technique for analyzing complex organic mixtures. Currently, there is no consensus normalization approach, nor an objective method for selecting one, for quantitative analyses of FT-ICR-MS data. We investigate a method to evaluate and score the amount of bias various normalization approaches introduce into the data.METHODS: We evaluate the ability of the Statistical Procedure for the Analysis of Normalization Strategies (SPANS) to guide selection of appropriate normalization approaches for two different FT-ICR-MS datasets. Further, we test the robustness of SPANS results to changes in SPANS parameter values and assess the impact of using various normalization approaches on downstream statistical analyses.
    RESULTS: The normalization approach identified by SPANS differed for the two datasets. Normalization methods impacted the statistical significance of peaks differently, underscoring the importance of carefully evaluating potential methods. More consistent SPANS scores resulted when at least 120 significant peaks are used, where larger sets of peaks were obtained by increasing the p-value threshold. Interestingly, we show that Total Sum Scaling and highest peak normalization, used in previous studies, underperformed relative to SPANS-recommended normalization approaches.
    CONCLUSIONS: While there is no single, best normalization method for all datasets, SPANS provides a mechanism to identify an appropriate normalization method for analyzing FT-ICR-MS data quantitatively. The number of peaks used in the background distributions of SPANS contributes more significantly to the reproducibility of results than the p-value thresholds used to obtain those peaks.
    DOI:  https://doi.org/10.1002/rcm.9068
  11. Talanta. 2021 Apr 01. pii: S0039-9140(20)31339-4. [Epub ahead of print]225 122048
    Puchalska P, Nelson AB, Stagg DB, Crawford PA.
      Efforts to enhance wellness and ameliorate disease via nutritional, chronobiological, and pharmacological interventions have markedly intensified interest in ketone body metabolism. The two ketone body redox partners, acetoacetate (AcAc) and D-β-hydroxybutyrate (D-βOHB) serve distinct metabolic and signaling roles in biological systems. A highly efficient, specific, and reliable approach to simultaneously quantify AcAc and D-βOHB in biological specimens is lacking, due to challenges of separating the structural isomers and enantiomers of βOHB, and to the chemical instability of AcAc. Here we present a single UPLC-MS/MS method that simultaneously quantifies both AcAc and βOHB using independent stable isotope internal standards for both ketones. This method incorporates one sample preparation step requiring only 7 min of analysis per sample. The output is linear over three orders of magnitude, shows very low limits of detection and quantification, is highly specific, and shows favorable recovery yields from mammalian serum and tissue samples. Tandem MS discriminates D-βOHB from structural isomers 2- or 4-hydroxybutyrate as well as 3-hydroxyisobutyrate (3-HIB). Finally, a simple derivatization distinguishes D- and L-enantiomers of βOHB, 3-HIB, and 2-OHB, using the same rapid chromatographic platform. Together, this simple, efficient, reproducible, scalable, and all-encompassing method will support basic and clinical research laboratories interrogating ketone metabolism and redox biochemistry.
    Keywords:  Acetoacetate instability; Acetoacetate internal standard; D-beta-hydroxybutyrate structural and stereo-isomers; Quantification of ketone bodies; UPLC-MS/MS
    DOI:  https://doi.org/10.1016/j.talanta.2020.122048
  12. J Chromatogr A. 2021 Jan 30. pii: S0021-9673(21)00066-2. [Epub ahead of print]1640 461942
    Lou D, Wang Y, Yang Q, Hu L, Zhu Q.
      Recent years have seen the field of extracellular vesicle (EV) studies burgeoning. This is mainly because EV constituents including nucleic acid, proteins, lipids, and metabolites are promising sources towards disease biomarker discovery. However, EV study remains challenging due to the complexity of biofluids as well as technical limitations during sample preparation. Here, we proposed a simple method combing ultrafiltration (UF) and phospholipid affinity to collect high purity EVs from 30 mL of urine sample for their metabolomic profiling. Ultracentrifugation (UC) for EV isolation was applied as a reference method. Western blot (WB) analysis, nanoparticles tracking analysis (NTA) and electron microscopy (EM) were used to assess EV protein markers and to characterize vesicle size and morphology. The results revealed that more than 1010 EV particles could be isolated from a 30 mL urine sample by the proposed method, and the resulting EVs carry specific protein markers and had a typical "cup shape" morphology. This suggests that our method is suitable for EV isolation and can provide sufficient EV quantity to ensure downstream analysis. Further untargeted metabolomic profiling of isolated EVs by UHPLC-QTOF-MS detected 433 metabolites by our methods and 432 metabolites by UC with a MS/MS similarity score greater than 0.7. We then applied the lipid metabolites-targeted method using UHPLC-QTrap-MS with the MRM mode, which successfully detected 467 compounds from urine EVs. This indicates that UF integrating phospholipid affinity is a reliable method for metabolic analysis of urinary EVs, which holds the potential for EV clinical application towards biomarker investigation from their metabolites.
    Keywords:  Extracellular vesicle; Lipidomic profiling; Metabolomic profiling; Phospholipid affinity; Ultracentrifugation
    DOI:  https://doi.org/10.1016/j.chroma.2021.461942
  13. Amino Acids. 2021 Feb 14.
    Opekar S, Zahradníčková H, Vodrážka P, Řimnáčová L, Šimek P, Moos M.
      L-amino acids (L-AAs) play different important roles in the physiology of all living organisms. Their chiral counterparts, D-amino acids (D-AAs) are increasingly being recognized as essential molecules in many biological systems. Secondary amino acids with cyclic structures, such as prolines, exhibit conformational rigidity and thus unique properties in the structural and protein folding. Despite their widespread occurrence, much less attention was paid to their chiral analysis, particularly when the minor, typically D-enantiomer, is present in low amounts in a complex biological matrix. In this paper, a cost-effective, chiral GC-MS method is described for capillary Chirasil-L-Val separation of nine cyclic secondary amino acid enantiomers with four-, five-, and six-membered rings, involving azetidine-2-carboxylic acid, pipecolic acid, nipecotic acid, proline, isomeric cis/trans 3-hydroxy, 4-hydroxyproline, and cis/trans-5-hydroxy-L-pipecolic acid in the excess of its enantiomeric antipode. The sample preparation involves in-situ derivatization with heptafluorobutyl chloroformate, simultaneous liquid-liquid micro-extraction into isooctane followed by amidation of the arising low-polar derivatives with methylamine, an evaporation step, re-dissolution, and final GC-MS analysis. The developed method was used for analyses of human biofluids, biologically active peptides containing chiral proline constituents, and collagen.
    Keywords:  Enantiomeric separation; GC–MS; Heptafluorobutyl chloroformate; Imino acids; Methyl amide derivatives; Secondary amino acids
    DOI:  https://doi.org/10.1007/s00726-021-02949-1