bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2021‒05‒23
twelve papers selected by
Sofia Costa
Cold Spring Harbor Laboratory

  1. Clin Chem Lab Med. 2021 May 19.
      OBJECTIVES: Clinical evaluation of vitamin D status is conventionally performed by measuring serum levels of a single vitamin D metabolite, 25-hydroxyvitamin D predominantly by immunoassay methodology. However, this neglects the complex metabolic pathways involved in vitamin D bioactivity, including two canonical forms D3 and D2, bioactive 1,25-dihydroxy metabolites and inactive 24-hydroxy and other metabolites.METHODS: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) can measure multiple analytes in a sample during a single run with high sensitivity and reference level specificity. We therefore aimed to develop and validate a LC-MS/MS method to measure simultaneously 13 circulating vitamin D metabolites and apply it to 103 human serum samples.
    RESULTS: The LC-MS/MS method using a Cookson-type derivatization reagent phenyl-1,2,4-triazoline-3,5-dione (PTAD) quantifies 13 vitamin D metabolites, including mono and dihydroxy-metabolites, as well as CYP11A1-derived D3 and D2 metabolites in a single run. The lower limit of quantitation was 12.5 pg/mL for 1,25(OH)2D3 with accuracy verified by analysis of National Institute of Standards and Technology (NIST) 972a standards. Quantification of seven metabolites (25(OH)D3, 25(OH)D2, 3-epi-25(OH)D3, 20(OH)D3, 24,25(OH)2D3, 1,25(OH)2D3 and 1,20S(OH)2D3) was consistently achieved in human serum samples.
    CONCLUSIONS: This profiling method can provide new insight into circulating vitamin D metabolite pathways forming the basis for improved understanding of the role of vitamin D in health and disease.
    Keywords:  liquid chromatography; mass spectrometry; metabolism; vitamin D
  2. J Chromatogr A. 2021 May 03. pii: S0021-9673(21)00333-2. [Epub ahead of print]1648 462209
      Two commercial stationary phases allowing both reversed phase mechanism and anion-exchange with different selectivity, i.e. CSH C18 and Atlantis PREMIER BEH C18 AX, were tested for the separation of a complex mixture of 21 fatty acids (FAs) encompassing saturated medium-, long- and very long chain FAs, unsaturated long and very long chain FAs, cis/trans isomers, and isomers of odd- and branched-chain FAs. For this purpose, the role of surface area of stationary phase and the effect of pH of the mobile phase on the retention of the analytes were investigated. Separation was performed by ultra-high-performance liquid chromatography coupled with high resolution mass spectrometry (UHPLC-HRMS). BEH C18 AX was shown to be more versatile and to offer superior retention of these analytes to CSH C18 owing to a higher surface area and anion-exchange capacity up to pH 8.5. The UHPLC system allows shortening analysis time, the chromatographic analysis being accomplished in about 5 min, affording a high throughput of samples without the need for derivatization or ion-pairing reagents compared to techniques based upon gas chromatography approaches or LC. Finally, the application of the BEH C18 AX column using UHPLC-HRMS was demonstrated for the separation and unambiguous identification of FAs of nutritional interest in a dietary supplement sample.
    Keywords:  Long chain fatty acids; Mixed mode-chromatography; Ultra-high-performance liquid chromatography–mass spectrometry; Very long chain fatty acids
  3. Nucleic Acids Res. 2021 May 21. pii: gkab382. [Epub ahead of print]
      Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. Here we introduce MetaboAnalyst version 5.0, aiming to narrow the gap from raw data to functional insights for global metabolomics based on high-resolution mass spectrometry (HRMS). Three modules have been developed to help achieve this goal, including: (i) a LC-MS Spectra Processing module which offers an easy-to-use pipeline that can perform automated parameter optimization and resumable analysis to significantly lower the barriers to LC-MS1 spectra processing; (ii) a Functional Analysis module which expands the previous MS Peaks to Pathways module to allow users to intuitively select any peak groups of interest and evaluate their enrichment of potential functions as defined by metabolic pathways and metabolite sets; (iii) a Functional Meta-Analysis module to combine multiple global metabolomics datasets obtained under complementary conditions or from similar studies to arrive at comprehensive functional insights. There are many other new functions including weighted joint-pathway analysis, data-driven network analysis, batch effect correction, merging technical replicates, improved compound name matching, etc. The web interface, graphics and underlying codebase have also been refactored to improve performance and user experience. At the end of an analysis session, users can now easily switch to other compatible modules for a more streamlined data analysis. MetaboAnalyst 5.0 is freely available at
  4. Anal Chem. 2021 May 20.
      In mass spectrometry, reliable quantification requires correction for variations in ionization efficiency between samples. The preferred method is the addition of a stable isotope-labeled internal standard (SIL-IS). In targeted metabolomics, a dedicated SIL-IS for each metabolite of interest may not always be realized due to high cost or limited availability. We recently completed the analysis of more than 70 biomarkers, each with a matching SIL-IS, across four mass spectrometry-based platforms (one GC-MS/MS and three LC-MS/MS). Using data from calibrator and quality control samples added to 60 96-well trays (analytical runs), we calculated analytical precision (CV) retrospectively. The use of integrated peak areas for all metabolites and internal standards allowed us to calculate precision for all matching analyte (A)/SIL-IS (IS) pairs as well as for all nonmatching A/IS pairs within each platform (total n = 1442). The median between-run precision for matching A/IS across the four platforms was 2.7-5.9%. The median CV for nonmatching A/IS (corresponding to pairing analytes with a non-SIL-IS) was 2.9-10.7 percentage points higher. Across all platforms, CVs for nonmatching A/IS increased with increasing difference in retention time (Spearman's rho of 0.17-0.93). The CV difference for nonmatching vs matching A/IS was often, but not always, smaller when analytes and internal standards were close structural analogs.
  5. J Biochem. 2021 May 01. pii: mvab054. [Epub ahead of print]
      Fatty acids (FAs) play important roles in several physiological and pathophysiological processes, functioning as both non-esterified free FAs (FFAs) and components of other lipid classes. Although many lipid classes are readily measured using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), the measurement of FFAs by this method is not straightforward because of inconsistent fragmentation behaviors. In this study, we describe a strategy to measure FFAs using conventional reverse-phase LC-ESI-MS/MS, without derivatization. The strategy combines three key methods: 1) an isocratic LC separation with a high organic solvent ratio, 2) post-column base addition, and 3) pseudo-multiple reaction monitoring. The method facilitates the measurement of ultra-long-chain FAs, the accumulation of which is a common biochemical abnormality in peroxisomal disorders. This study delivers a broad strategy that measures a wide spectrum of FFA species in complex biological samples.
    Keywords:  LC–MS/MS; ammonium hydroxide; free fatty acid; isocratic LC; pseudo MRM
  6. J Anal Toxicol. 2021 May 20. pii: bkab052. [Epub ahead of print]
      Analytical performance of stable isotope labeled internal standardization (SIL-IS) and threshold accurate calibration (TAC) methods of matrix normalization are compared for quantitation of 51 drugs and metabolites (analytes) in urine with analysis by UPLC-MS-MS. SIL-IS was performed with both analyte-specific (ASIL-IS) and shared (SSIL-IS) internal standards. Variance in inter-specimen matrix effect, without use of a matrix normalization method, was studied by UPLC-MS-MS (Ultra Performance Liquid Chromatography with tandem mass spectrometry) analysis of 338 urine donor samples and showed over 200% variation in ion response for some analytes. Matrix normalization methods were evaluated for precision, accuracy, calibration, multi-matrix recovery and positive casework quantitation. Acceptable calibration and quality control criteria were achieved for all methods when calibrators and controls were prepared from the same urine matrix pool. Quantitative accuracy, determined by addition of analytes to multi-donor urine pools at two concentration levels, resulted in acceptable percent relative standard deviation (%RSD) and bias for TAC and ASIL-IS methods. SSIL-IS method quantitations in analyte-supplemented donor pools revealed a %RSD ranging from 20-60% for more than 30% of the analytes and a method bias that ranged up to 87%, with a differential matrix effect on analyte and shared internal standard accounting for the imprecision and bias. Analyte quantitation in 162 authentic case samples showed close agreement for TAC and ASIL-IS methods, with greater variance in the SSIL-IS method. The study demonstrates effective matrix normalization by ASIL-IS and TAC methods and a matrix-caused bias in the SSIL-IS method.
    Keywords:  matrix normalization; urine drug monitoring
  7. J Vis Exp. 2021 Apr 27.
      Sphingolipids are cellular components that have well-established roles in human metabolism and disease. Mass spectrometry can be used to determine whether sphingolipids are altered in a disease and investigate whether sphingolipids can be targeted clinically. However, properly powered prospective studies that acquire tissues directly from the surgical suite can be time consuming, and technically, logistically, and administratively challenging. In contrast, retrospective studies can take advantage of cryopreserved human specimens already available, usually in large numbers, at tissue biorepositories. Other advantages of procuring tissues from biorepositories include access to information associated with the tissue specimens including histology, pathology, and in some instances clinicopathological variables, all of which can be used to examine correlations with lipidomics data. However, technical limitations related to the incompatibility of optimal cutting temperature compound (OCT) used in the cryopreservation and mass spectrometry is a technical barrier for the analysis of lipids. However, we have previously shown that OCT can be easily removed from human biorepository specimens through cycles of washes and centrifugation without altering their sphingolipid content. We have also previously established that sphingolipids in human tissues cryopreserved in OCT are stable for up to 16 years. In this report, we outline the steps and workflow to analyze sphingolipids in human tissue specimens that are embedded in OCT, including washing tissues, weighing tissues for data normalization, the extraction of lipids, preparation of samples for analysis by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), mass spectrometry data integration, data normalization, and data analysis.
  8. J Am Soc Mass Spectrom. 2021 May 20.
      Up to 80% of the fatty acids in Staphylococcus aureus membrane lipids are branched, rather than straight-chain, fatty acids. The branched fatty acids (BCFAs) may have either an even or odd number of carbons, and the branch position may be at the penultimate carbon (iso) or the antepenultimate (anteiso) carbon of the tail. This results in two sets of isomeric fatty acid species with the same number of carbons that cannot be resolved by mass spectrometry. The isomer/isobar challenge is further complicated when the mixture of BCFAs and straight-chain fatty acids (SCFAs) are esterified into diacylated lipids such as the phosphatidylglycerol (PG) species of the S. aureus membrane. No conventional chromatographic method has been able to resolve diacylated lipids containing mixtures of SCFAs, anteiso-odd, iso-odd, and iso-even BCFAs. A major hurdle to method development in this area is the lack of relevant analytical standards for lipids containing BCFA isomers. The diversity of the S. aureus lipidome and its naturally high levels of BCFAs present an opportunity to explore the potential of resolving diacylated lipids containing BCFAs and SFCAs. Using our knowledge of lipid and fatty acid biosynthesis in S. aureus, we have used a stable-isotope-labeling strategy to develop and validate a 30 min C18 reversed-phase liquid chromatography method combined with traveling-wave ion mobility-mass spectrometry to provide resolution of diacylated lipids based on the number of BCFAs that they contain.
    Keywords:  Staphylococcus aureus; branched fatty acids; isomers; isotope labeling; lipids; reversed-phase liquid chromatography
  9. J Chromatogr B Analyt Technol Biomed Life Sci. 2021 May 01. pii: S1570-0232(21)00219-1. [Epub ahead of print]1175 122739
      Lipid analysis is a powerful tool that can elucidate the pathogenic roles of lipids in metabolic diseases, and facilitate the development of potential biomarkers. Lipid analysis by large-scale lipidomics requires a high-speed and high-throughput analytical platform. In the present study, a high-speed analytical method for lipid analysis using nanoflow ultrahigh-performance liquid chromatography-electrospray ionisation-tandem mass spectrometry (nUHPLC-ESI-MS/MS) was optimised by investigating the effects of column flow rate, pump flow rate, dwell time, initial binary mobile phase composition, and gradient duration on the separation efficiency of standard lipid mixtures. The minimum gradient time for high-speed lipid separation was determined by examining the time-based separation efficiency and spectral overlap of isobaric lipid species during selected reaction monitoring-based quantification of sphingomyelin and a second isotope of phosphatidylcholine, which differ in molecular weight by only 1 Da. Finally, the optimised nUHPLC-ESI-MS/MS method was applied to analyse 200 plasma samples from patients with liver, gastric, lung, and colorectal cancer to evaluate its performance by measuring previously identified candidate lipid biomarkers. About 73% of the reported marker candidates (6 out of 7 in liver, 5/9 in gastric, 4/6 in lung, and 6/7 in colorectal cancer) could be assigned using the optimised method, supporting its use for high-throughput lipid analysis.
    Keywords:  Blood plasma; Cancer; High-speed lipid analysis; Lipidomics; nUHPLC-ESI-MS/MS
  10. Comput Struct Biotechnol J. 2021 ;19 1956-1965
      Principal component analysis (PCA) is a useful tool for omics analysis to identify underlying factors and visualize relationships between biomarkers. However, this approach is limited in addressing life complexity and further improvement is required. This study aimed to develop a new approach that combines mass spectrometry-based metabolomics with multiblock PCA to elucidate the whole-body global metabolic network, thereby generating comparable metabolite maps to clarify the metabolic relationships among several organs. To evaluate the newly developed method, Zucker diabetic fatty (ZDF) rats (n = 6) were used as type 2 diabetic models and Sprague Dawley (SD) rats (n = 6) as controls. Metabolites in the heart, kidney, and liver were analyzed by capillary electrophoresis and liquid chromatography mass spectrometry, respectively, and the detected metabolites were analyzed by multiblock PCA. More than 300 metabolites were detected in the heart, kidney, and liver. When the metabolites obtained from the three organs were analyzed with multiblock PCA, the score and loading maps obtained were highly synchronized and their metabolism patterns were visually comparable. A significant finding in this study was the different expression patterns in lipid metabolism among the three organs; notably triacylglycerols with polyunsaturated fatty acids or less unsaturated fatty acids showed specific accumulation patterns depending on the organs.
    Keywords:  AMP, adenosine monophosphate; Biomarkers; CE/MS, capillary electrophoresis mass spectrometry; CV, coefficient of variation; ESI, electrospray ionization; FABP, fatty acid-binding protein; GC/MS, gas chromatography mass spectrometry; LC/MS, liquid chromatography mass spectrometry; Mass spectrometry; Metabolomics; Multiblock PCA; PCA, principal component analysis; PPAR, peroxisome proliferator-activated receptor; QC, quality control; SD, Sprague Dawley; TCA, tricarboxylic acid. CoA, coenzyme A; TG, triacylglycerol; Type 2 Diabetes; UPLC, ultra-performance liquid chromatography; ZDF, Zucker diabetic fatty
  11. Anal Chem. 2021 May 19.
      Analytical methods that allow rapid, sensitive, and specific chemical measurements are central to forensic analysis and essential to accelerating compound screening and confirmation. We have previously reported the development of the MasSpec Pen technology as an easy-to-use and disposable hand-held device integrated to a mass spectrometer for direct analysis and molecular profiling of biological samples. In this Technical Note, we describe a new apparatus that integrates the MasSpec Pen device with a subatmospheric pressure chemical ionization (sub-APCI) source and an ion trap mass spectrometer for detection and semiquantitative analysis of forensic-related compounds. Coupling the MasSpec Pen device to a sub-APCI source allowed semiquantitative analysis of the drugs cocaine and oxycodone, the agrochemicals atrazine and azoxystrobin, and the explosives trinitrotoluene and dinitroglycerin in under 20 s. Using chemical ionization, improved reproducibility and sensitivity for targeted chemical detection and compound identification was achieved while maintaining the user-friendly features of the hand-held MasSpec Pen device. Limits of detection in the high picogram to low nanogram range were obtained for the compounds analyzed, which are within the range of federal screening cutoffs and those reported for other ambient ionization MS techniques. Altogether, the MasSpec Pen sub-APCI system described enabled rapid and semiquantitative chemical analysis for forensic applications and could be further adapted and applied to other areas of chemical testing.
  12. J Chromatogr A. 2021 May 02. pii: S0021-9673(21)00339-3. [Epub ahead of print]1648 462215
      A new analyte separation and preconcentration method for the trace determination of antidepressant drugs, Fluoxetine (FLU) and Citalopram (CIT) in urine and wastewaters, was developed based on HPLC-DAD analysis after magnetic solid phase extraction (MSPE). In the proposed method, FLU and CIT were retained on the newly synthetized magnetic sorbent (Fe3O4@PPy-GO) in the presence of buffer (pH 10.0) and then were desorbed into a lower volume of acetonitrile prior to the chromatographic determinations. Before HPLC analysis, all samples were filtered through a 0.45 µm PTFE filter. Experimental parameters such as interaction time, desorption solvent and volume, and pH were studied and optimized in order to establish the detection limit, linearity, enrichment factor and other analytical figures of merit under optimum operation conditions. In the developed method, FLU and CIT were analyzed by diode array detector at the corresponding maximum wavelengths of 227 and 238 nm, respectively, by using an isocratic elution of 60% pH 3.0 buffer, 30% acetonitrile, and 10% methanol. By using the optimum conditions, limit of detections for FLU and CIT were 1.58 and 1.43 ng mL-1, respectively, while the limit of quantifications was 4.82 and 4.71 ng mL-1, respectively. Relative standard deviations (RSD%) for triplicate analyses of model solutions containing 100 ng mL-1 target molecules were found to be less than 5.0 %. Finally, the method was successfully applied to urine (both simulated and real healthy human) and wastewater samples, and quantitative results were obtained in recovery experiments.
    Keywords:  Fluoxetine, Citalopram; HPLC; Magnetic solid phase extraction; Urine samples, Environmental water samples