bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2020–02–02
nine papers selected by
Sofia Costa, Cold Spring Harbor Laboratory
  1. Derivatization strategy combined with parallel reaction monitoring for the characterization of short-chain fatty acids and their hydroxylated derivatives in mouse.
  2. Chromatographic HILIC indexes to characterize the lipophilicity of zwitterions.
  3. Considerations for mass spectrometry based multi-omic analysis of clinical samples.
  4. Rapid and miniaturized qualitative and quantitative gas chromatography profiling of human blood total fatty acids.
  5. Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.
  6. Targeted metabolomics: Liquid chromatography coupled to mass spectrometry method development and validation for the identification and quantitation of modified nucleosides as putative cancer biomarkers.
  7. New Frontiers in Lipidomics Analyses using Structurally Selective Ion Mobility-Mass Spectrometry.
  8. Special Issue on "NMR-Based Metabolomics and Its Applications Volume 2".
  9. In-tube solid-phase microextraction with a dummy molecularly imprinted monolithic capillary coupled to ultra-performance liquid chromatography-tandem mass spectrometry to determine cannabinoids in plasma samples.
  1. Anal Chim Acta. 2020 Mar 01. pii: S0003-2670(19)31352-2. [Epub ahead of print]1100 66-74
    Derivatization strategy combined with parallel reaction monitoring for the characterization of short-chain fatty acids and their hydroxylated derivatives in mouse.
    Juntong Wei, Li Xiang, Xiaona Li, Yuanyuan Song, Chunxue Yang, Fenfen Ji, Arthur Chi Kong Chung, Kun Li, Zian Lin, Zongwei Cai.
      Short-chain fatty acids (SCFAs) and hydroxylated short-chain fatty acids (OH-SCFAs) are crucial intermediates related to a variety of diseases, such as bowel disease, cardiovascular disease, renal disease and cancer. A global profiling method to screen SCFAs and OH-SCFAs was developed by tagging these analytes with d0/d6-N, N-dimethyl-6,7-dihydro-5H-pyrrolo [3,4-d] pyrimidine-2-amine (d0/d6-DHPP) and using ultra-high performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-MS/MS) in parallel reaction monitoring (PRM) mode. The derivatization procedure was simple and rapid. The targeted compounds could be derivatized within 3 min under mild condition and analyzed without the need of further purification. The derivatization significantly improved the chromatographic performance and mass spectrometry response. The d6-DHPP tagged standards were used as internal standards, which remarkably reduced the matrix effects. The use of high resolution PRM mode made it possible to locate unknown SCFA and OH-SCFA species, and greatly reduced the false positive identification results. The developed method was successfully applied to the analysis of mouse fecal, serum, and liver tissue samples harvested from the breast cancer nude mice that had been exposed with 2,2',4,4'-tetrabromodiphenyl ether (BDE-47). Results showed that 40 analytes (10 SCFAs and 30 OH-SCFAs) were characterized. Semi-quantitative analysis indicated that the exposure of BDE-47 to the mice altered the SCFA and OH-SCFA metabolism, especially in the high dose group. This study provides a high-throughput method to characterize SCFAs and OH-SCFAs in mouse samples.
    Keywords:  2,2′,4,4′-Tetrabromodiphenyl ether; Derivatization; Hydroxylated short-chain fatty acids; Parallel reaction monitoring; Short-chain fatty acids
    DOI:  https://doi.org/10.1016/j.aca.2019.11.009
  2. Eur J Pharm Sci. 2020 Jan 23. pii: S0928-0987(20)30021-X. [Epub ahead of print] 105232
    Chromatographic HILIC indexes to characterize the lipophilicity of zwitterions.
    Maura Vallaro, Giuseppe Ermondi, Giulia Caron.
      Reverse phase high pressure liquid chromatography (RP-HPLC) is widely employed in drug discovery for lipophilicity measurements. Hydrophilic interaction liquid chromatography (HILIC) may represent a good alternative to RP-HPLC in the determination of the lipophilicity of hydrophilic compounds like zwitterions. In this paper three different HILIC stationary phases (ZIC®-HILIC, ZIC®-pHILIC and ZIC®-cHILIC) and two different mobile phases (80%ACN/20%buffer and 90%ACN/10%buffer) were combined to set-up six chromatographic systems. A computational tool named Block Relevance (BR) analysis was firstly used to deconvolute the balance of intermolecular forces governing retention in the six systems. Then the lipophilicity profiles (log k vs pH) of ten model ampholytes were determined. Results support that the lipophilicity of zwitterions at any pH can be successfully determined with a ZIC®-cHILIC stationary phase and an 80%ACN/20%buffer mobile phase. To extend the dataset and confirm results, a second series of zwitterionic drugs was also analysed.
    Keywords:  Ampholytes; BR analysis; HILIC; lipophilicity; zwitterions
    DOI:  https://doi.org/10.1016/j.ejps.2020.105232
  3. Expert Rev Proteomics. 2020 Jan 29.
    Considerations for mass spectrometry based multi-omic analysis of clinical samples.
    Esei T Teclemariam, Melissa R Pergande, Stephanie M Cologna.
      Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid and metabolite composition of an array of biospecimens. With this increase in the number - omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas Covered: In this short review, we outline considerations for working with clinical (e.g., human) specimens including blood, urine and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert Opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and being able to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.
    Keywords:  Mass spectrometry; clinical; lipidomics; metabolomics; proteomics; translational
    DOI:  https://doi.org/10.1080/14789450.2020.1724540
  4. Anal Bioanal Chem. 2020 Jan 30.
    Rapid and miniaturized qualitative and quantitative gas chromatography profiling of human blood total fatty acids.
    Giuseppe Micalizzi, Emanuela Ragosta, Sara Farnetti, Paola Dugo, Peter Q Tranchida, Luigi Mondello, Francesca Rigano.
      The qualitative and quantitative profiling of fatty acids in human blood is a useful tool in disease prevention and health care, two concepts that are intimately related. In fact, fatty acid (FA) analysis can provide in-depth information on a specific metabolic state of individuals. The goal of the present research consisted of the development of a rapid and miniaturized analytical strategy for the complete characterization of the fatty acid profile in human blood. Sample collection was carried out by using the dried blood spot approach, while fatty acid derivatization to methyl esters was performed directly by using sodium methoxide and boron trifluoride. The following figures of merit were defined: intra- and inter-day repeatability, linearity range, limits of detection, and quantification. Additionally, the accuracy of the developed method was evaluated in the analysis of a certified reference human plasma sample. Apart from blood, the analytical procedure was also applied to samples of human serum and plasma. During the final stage of the research, the developed analytical method was performed in a fully automated manner. Graphical abstract.
    Keywords:  Direct derivatization; Dried blood spot; Fatty acid methyl esters; Human blood; Lipidomics
    DOI:  https://doi.org/10.1007/s00216-020-02424-y
  5. J Proteome Res. 2020 Jan 27.
    Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.
    Kendra J Adams, Brian Pratt, Neelanjan Bose, Laura G Dubois, Lisa St John-Williams, Kevin M Perrott, Karina Ky, Pankaj Kapahi, Vagisha Sharma, Michael J MacCoss, M Arthur Moseley, Carol A Colton, Brendan X MacLean, Birgit Schilling, J Will Thompson.
      Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source software tool for targeted quantitative mass spectrometry method development and data processing with a ten-year history supporting 6 major instrument vendors. Designed initially for proteomic analysis, we describe the expansion of Skyline to data for small molecule analysis, including selected reaction monitoring (SRM), high-resolution mass spectrometry (HRMS), and calibrated quantification. This fundamental expansion of Skyline from a peptide-sequence centric tool to a molecule-centric tool makes it agnostic to the source of the molecule while retaining Skyline features critical for workflows in both peptide and more general biomolecular research. The data visualization and interrogation features already available in Skyline - such as peak picking, chromatographic alignment, and transition selection - have been adapted to support small molecule data, including metabolomics. Herein, we explain the conceptual workflow for small molecule analysis using Skyline, demonstrate Skyline performance benchmarked against a comparable instrument vendor software tool, and present additional real-world applications. Further, we include step-by-step instructions on using Skyline for small molecule quantitative method development and data analysis on data acquired with a variety of mass spectrometers from multiple instrument vendors.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00640
  6. Talanta. 2020 Apr 01. pii: S0039-9140(19)31273-1. [Epub ahead of print]210 120640
    Targeted metabolomics: Liquid chromatography coupled to mass spectrometry method development and validation for the identification and quantitation of modified nucleosides as putative cancer biomarkers.
    Adriana Teixeira Godoy, Marcos Nogueira Eberlin, Ana Valéria Colnaghi Simionato.
      A notable change in the body fluids nucleosides of cancer patients has been actively highlighted in searches for new biomarkers to early cancer detection. For this reason, improvements of bioanalytical methods for these compounds focused on a noninvasive sampling trend are of great importance. Therefore, this work aimed firstly to develop efficient methods for nucleoside analysis in urine and serum by liquid chromatography-tandem mass spectrometry (LC-MS/MS), applying different strategies to quantify nine nucleosides, and further identify other untargeted nucleosides. Sample preparation was based on protein precipitation and affinity-solid phase extraction (SPE), whereas quantification was performed using a triple quadrupole (QqQ) mass analyzer operating in the selected reaction monitoring (SRM) mode. Surrogates matrices were proposed as an alternative to standard addition calibration. Specifically, to quantitate creatinine, a simple LC-MS/MS method was validated and used for normalization of urinary metabolites quantitation. To identify the other nucleosides, LC methods using different MS scans modes were evaluated on a quadrupole-time of flight (Q-TOF) or a hybrid triple quadrupole linear ion trap (Q-trap). Validation was performed for nucleosides quantification using the synthetic matrices of urine and serum, and selectivity, linearity, accuracy, reproducibility, matrix effect, LOD's and LOQ's were accessed, providing trustworthy results for bioanalysis purposes. Both LC-Q-Trap/MS and LC-Q-TOF/MS methods showed proper sensitivity for structural characterization on assays with urine and serum samples from healthy volunteers and could also be used in the identification of untargeted nucleosides. The investigated approaches delivered in-depth results and seem promising for future applications on urine and serum samples analyses aiming to validate nucleosides as cancer biomarkers.
    Keywords:  Blood serum; LC-MS/MS; Method development; Method validation; Nucleosides; Urine
    DOI:  https://doi.org/10.1016/j.talanta.2019.120640
  7. Trends Analyt Chem. 2019 Jul;116 316-323
    New Frontiers in Lipidomics Analyses using Structurally Selective Ion Mobility-Mass Spectrometry.
    Rachel A Harris, Katrina L Leaptrot, Jody C May, John A McLean.
      The growth of lipidomics and the high isomeric complexity of the lipidome has revealed a need for analytical techniques capable of structurally characterizing lipids with a high degree of specificity. Lipids are morphologically diverse molecules that can exist as any one of a large number of isomeric species, and as such are often indistinguishable by mass spectrometry without a complementary separation method. Recent developments in the field of lipidomics aim to address these challenges by utilizing a combination of multiple analytical techniques which are selective to lipid primary structure. This review summarizes two emerging strategies for lipidomic analysis, namely, ion mobility-mass spectrometry and ion fragmentation via ozonolysis.
    Keywords:  Lipids; collision cross section; ion mobility-mass spectrometry; isomers; lipidomics; mass spectrometry; molecular structure; ozonolysis
    DOI:  https://doi.org/10.1016/j.trac.2019.03.031
  8. Metabolites. 2020 Jan 26. pii: E45. [Epub ahead of print]10(2):
    Special Issue on "NMR-Based Metabolomics and Its Applications Volume 2".
    Flaminia Cesare Marincola, Luisa Mannina.
      Over the last decade, the number of scientific publications in the metabolomics area has increased exponentially. The literature includes ~29,000 contributions (articles and reviews) during the period of 2009-2019, revealing metabolomics applications in a wide range of fields, including medical, plant, animal, and food sciences (this bibliographic data were retrieved from the SCOPUS database, searching "metabolomics" in keywords). The high applicability of this approach is due to its ability to qualitatively and quantitatively characterize the chemical profile of all the low molecular weight metabolites (metabolome) present in cells, tissues, organs, and biological fluids as end products of the cellular regulatory pathways. Thus, providing a snapshot of the phenotype of a biological system, metabolomics offers useful contributions to a comprehensive insight into the functional status of human, animal, plant, and microbe organisms. The contributions collected in this Special Issue (12 articles, one review and one technical report) report on the recent technical advances and practical applications of NMR spectroscopy to metabolomics analyses.
    Keywords:  NMR; metabolomics
    DOI:  https://doi.org/10.3390/metabo10020045
  9. Anal Chim Acta. 2020 Feb 22. pii: S0003-2670(19)31361-3. [Epub ahead of print]1099 145-154
    In-tube solid-phase microextraction with a dummy molecularly imprinted monolithic capillary coupled to ultra-performance liquid chromatography-tandem mass spectrometry to determine cannabinoids in plasma samples.
    Camila Marchioni, Tatiana Manzini Vieira, Antônio Eduardo Miller Crotti, José Alexandre Crippa, Maria Eugênia Costa Queiroz.
      A selective and sensitive method that uses automated in-tube solid-phase microextraction coupled to ultra-performance liquid chromatography-tandem mass spectrometry (in-tube SPME/UHPLC-MS/MS) was developed to determine cannabidiol (CBD) and Δ9-tetrahydrocannabinol (Δ9-THC) in plasma samples. A new dummy molecularly imprinted monolithic capillary (MIP monolith) for in-tube SPME was prepared by in situ polymerization in a fused silica capillary; hydrogenated cannabidiol was employed as dummy template. Fourier Transform Infrared Spectroscopy (FTIR) confirmed that the synthesis reagents were incorporated into the polymer chain. On the basis of the microscopy images (scanning electron microscopy - SEM and transmission electron microscopy - TEM), the MIP monolithic phase presented larger pores than the non-imprinted monolithic phase (NIP monolith), as well as a skeleton comprising clusters consisting of microspheres. By optimizing the polymerization conditions, the MIP monolith specifically recognized CBD and Δ9-THC. The MIP monolith had CBD and Δ9-THC sorption capacity of 148.05 and 44.49 ng cm-3, respectively. The capillary was reused over fifty times without significant changes in its extraction efficiency. For both CBD and Δ9-THC, in-tube SPME/UHPLC-MS/MS presented linear range from 10 to 300 ng mL-1, precision with coefficient of variation (CV) values ranging from 0.2% to 19.1% (LLOQ), and accuracy with relative standard deviation (RSD) values spanning from -9.3% to 19.6% (LLOQ). The developed method was successfully applied to determine cannabinoid levels in plasma samples from volunteer patients in treatment with CBD.
    Keywords:  Cannabinoids; In-tube SPME; Molecularly imprinted monolith; Plasma samples
    DOI:  https://doi.org/10.1016/j.aca.2019.11.017
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