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Bohn T, Balbuena E, Ulus H, Iddir M, Wang G, Crook N, Eroglu A. Carotenoids in Health as Studied by Omics-Related Endpoints. Adv Nutr 2023; 14:1538-1578. [PMID: 37678712 PMCID: PMC10721521 DOI: 10.1016/j.advnut.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023] Open
Abstract
Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor κB and nuclear factor erythroid 2-related factor 2. Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor and peroxisome proliferator-activated receptors, which play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes and proteins implicated in oxidative stress and inflammation, antioxidation, and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)omics-related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, as well as metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells, or other tissue cellular extracts. In this review, we highlight the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.
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Affiliation(s)
- Torsten Bohn
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg.
| | - Emilio Balbuena
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Hande Ulus
- Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Mohammed Iddir
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Genan Wang
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Abdulkerim Eroglu
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States.
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2
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Gao S, Zhou X, Yue M, Zhu S, Liu Q, Zhao XE. Advances and perspectives in chemical isotope labeling-based mass spectrometry methods for metabolome and exposome analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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3
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Microflow LC-MS/MS to improve sensitivity for antisense oligonucleotides bioanalysis: critical role of sample cleanness. Bioanalysis 2022; 14:1365-1376. [PMID: 36625771 DOI: 10.4155/bio-2022-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background: Quantitative bioanalysis of antisense oligonucleotides (ASOs) is crucial to study their pharmacokinetic properties. An ultrasensitive bioanalytical method is often desired for quantifying low-concentration ASOs. Results: Effects of microflow LC and sample cleanness on sensitivity improvement of ASOs were evaluated. Sixfold sensitivity improvement of ASO-001 was achieved using microflow LC-MS/MS compared with conventional analytical flow method. Different sample extracts (hybridization, SPE and protein precipitation) were evaluated for sensitivity improvement by microflow LC. More sensitivity improvement was observed in the cleaner sample extract. Conclusion: Microflow LC increases sensitivity for ASO bioanalysis. The cleaner the sample extract, the better the sensitivity improvement. An ultrasensitive hybridization microflow LC-MS/MS method with lower limit of quantification of 0.100 ng/ml was developed and qualified for quantifying ASO-001 in plasma.
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Sowers ML, Tang H, Singh VK, Khan A, Mishra A, Restrepo BI, Jagannath C, Zhang K. Multi-OMICs analysis reveals metabolic and epigenetic changes associated with macrophage polarization. J Biol Chem 2022; 298:102418. [PMID: 36030823 PMCID: PMC9525912 DOI: 10.1016/j.jbc.2022.102418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022] Open
Abstract
Macrophages (MФ) are an essential immune cell for defense and repair that travel to different tissues and adapt based on local stimuli. A critical factor that may govern their polarization is the crosstalk between metabolism and epigenetics. However, simultaneous measurements of metabolites, epigenetics, and proteins (phenotype) have been a major technical challenge. To address this, we have developed a novel triomics approach using mass spectrometry to comprehensively analyze metabolites, proteins, and histone modifications in a single sample. To demonstrate this technique, we investigated the metabolic-epigenetic-phenotype axis following polarization of human blood–derived monocytes into either ‘proinflammatory M1-’ or ‘anti-inflammatory M2-’ MФs. We report here a complex relationship between arginine, tryptophan, glucose, and the citric acid cycle metabolism, protein and histone post-translational modifications, and human macrophage polarization that was previously not described. Surprisingly, M1-MФs had globally reduced histone acetylation levels but high levels of acetylated amino acids. This suggests acetyl-CoA was diverted, in part, toward acetylated amino acids. Consistent with this, stable isotope tracing of glucose revealed reduced usage of acetyl-CoA for histone acetylation in M1-MФs. Furthermore, isotope tracing also revealed MФs uncoupled glycolysis from the tricarboxylic acid cycle, as evidenced by poor isotope enrichment of succinate. M2-MФs had high levels of kynurenine and serotonin, which are reported to have immune-suppressive effects. Kynurenine is upstream of de novo NAD+ metabolism that is a necessary cofactor for Sirtuin-type histone deacetylases. Taken together, we demonstrate a complex interplay between metabolism and epigenetics that may ultimately influence cell phenotype.
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Affiliation(s)
- Mark L Sowers
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | - Hui Tang
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | - Vipul K Singh
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | - Arshad Khan
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | - Abhishek Mishra
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | | | - Chinnaswamy Jagannath
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX.
| | - Kangling Zhang
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX.
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5
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Mostafa ME, Grinias JP, Edwards JL. Evaluation of Nanospray Capillary LC-MS Performance for Metabolomic Analysis in Complex Biological Matrices. J Chromatogr A 2022; 1670:462952. [DOI: 10.1016/j.chroma.2022.462952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 11/29/2022]
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6
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Shan L, Jones B. Nano liquid chromatography, an updated review. Biomed Chromatogr 2022; 36:e5317. [PMID: 34981550 DOI: 10.1002/bmc.5317] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 11/11/2022]
Abstract
Low flow chromatography has a rich history of innovation but has yet to reach widespread implementation in bioanalytical applications. Improvements in pump technology, microfluidic connections, and nano-electrospray sources for mass spectrometry have laid the groundwork for broader application, and innovation in this space has accelerated in recent years. This article reviews the instrumentation used for nano-flow liquid chromatography , the types of columns employed, and strategies for multi-dimensionality of separations, which is key to the future state of the technique to the high-throughput needs of modern bioanalysis. An update of the current applications where nano-LC is widely used, such as proteomics and metabolomics, is discussed. But the trend towards biopharmaceutical development of increasingly complex, targeted, and potent therapeutics for the safe treatment of disease drives the need for ultimate selectivity and sensitivity of our analytical platforms for targeted quantitation in a regulated space. The selectivity needs are best addressed by mass spectrometric detection, especially at high resolutions, and exquisite sensitivity is provided by nano-electrospray ionization as the technology continues to evolve into an accessible, robust, and easy to use platform.
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7
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Ni HT, Prabhu GRD, Elpa DP, Chiu HY, Urban PL. Flat Disc-Shaped Sampling Probe and Online Re-extraction Apparatus for Mass Spectrometric Analysis of Skin Metabolites: A Proof of Concept. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2803-2811. [PMID: 34739241 DOI: 10.1021/jasms.1c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sweat analysis provides an alternative and noninvasive way of clinical diagnostics. However, sampling and transferring sweat-derived samples to analytical instruments is challenging. In this report, we demonstrate a method utilizing a flat disc-shaped sampling probe, and a compatible re-extraction apparatus coupled online with extractive electrospray ionization (EESI) mass spectrometry (MS). The probe enables sampling of metabolites from a skin area of ∼2.2 cm2. The subsequent online re-extraction and analysis by EESI-MS further mitigates matrix effects caused by sweat components, thus eliminating sample preparation steps. The total analysis time is only 6 min. We have optimized the key parameters of the system, including flow rate of the nebulizing gas in ESI, pressure of the nebulizing gas in pneumatic sample nebulizer, flow rate of the solvent in ESI, and composition of extractant. The standard solutions (0.1 mL) were supplemented with 0.04 M sodium chloride to mimic the matrix effect normally observed in sweat samples. The method has been characterized with four chemical standards (positive-ion mode of histidine, leucine, urocanic acid; negative-ion mode of lactic acid). The limits of detection range from 1.09 to 95.9 nmol. We have further demonstrated the suitability of the method for analysis of sweat. An attempt was made to identify some of the recorded signals by product-ion scan and accurate/exact mass matching.
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Affiliation(s)
- Hsiang-Ting Ni
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Gurpur Rakesh D Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Decibel P Elpa
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Hsien-Yi Chiu
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, 25 Jingguo Road, Hsinchu, 300, Taiwan
- Department of Dermatology, National Taiwan University Hospital Hsin-Chu Branch, 25 Jingguo Road, Hsinchu 300, Taiwan
- Department of Dermatology, National Taiwan University Hospital, 7 Chung Shan S. Road, Taipei 100, Taiwan
- Department of Dermatology, College of Medicine, National Taiwan University, 1 Jen Ai Road, Taipei 100, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Road., Hsinchu 30013, Taiwan
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8
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Sweat metabolome and proteome: Recent trends in analytical advances and potential biological functions. J Proteomics 2021; 246:104310. [PMID: 34198014 DOI: 10.1016/j.jprot.2021.104310] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 12/11/2022]
Abstract
Metabolome and proteome profiling of biofluids, e.g., urine, plasma, has generated vast and ever-increasing amounts of knowledge over the last few decades. Paradoxically, omics analyses of sweat, one of the most readily available human biofluids, have lagged behind. This review capitalizes on the current knowledge and state of the art analytical advances of sweat metabolomics and proteomics. Moreover, current applications of sweat omics such as the discovery of disease biomarkers and monitoring athletic performance are also presented in this review. Another area of emerging knowledge that has been highlighted herein lies in the role of skin host-microbiome interactions in shaping the sweat metabolite-protein profiles. Discussion of future research directions describes the need to have a better grasp of sweat chemicals and to better understand how they function as aided by advances in omics tools. Overall, the role of sweat as an information-rich biofluid that could complement the exploration of the skin metabolome/proteome is emphasized.
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9
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Zaikin VG, Borisov RS. Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. Crit Rev Anal Chem 2021; 52:1287-1342. [PMID: 33557614 DOI: 10.1080/10408347.2021.1873100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.
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Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
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10
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Xiao L, Wang C, Dai C, Littlepage LE, Li J, Schultz ZD. Untargeted Tumor Metabolomics with Liquid Chromatography-Surface-Enhanced Raman Spectroscopy. Angew Chem Int Ed Engl 2020; 59:3439-3443. [PMID: 31765069 PMCID: PMC7028501 DOI: 10.1002/anie.201912387] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Metabolomics is a powerful systems biology approach that monitors changes in biomolecule concentrations to diagnose and monitor health and disease. However, leading metabolomics technologies, such as NMR and mass spectrometry (MS), access only a small portion of the metabolome. Now an approach is presented that uses the high sensitivity and chemical specificity of surface-enhanced Raman scattering (SERS) for online detection of metabolites from tumor lysates following liquid chromatography (LC). The results demonstrate that this LC-SERS approach has metabolite detection capabilities comparable to the state-of-art LC-MS but suggest a selectivity for the detection of a different subset of metabolites. Analysis of replicate LC-SERS experiments exhibit reproducible metabolite patterns that can be converted into barcodes, which can differentiate different tumor models. Our work demonstrates the potential of LC-SERS technology for metabolomics-based diagnosis and treatment of cancer.
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Affiliation(s)
- Lifu Xiao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Chuanqi Wang
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, South Bend, IN 46617
| | - Chen Dai
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, South Bend, IN 46617
| | - Laurie E Littlepage
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, South Bend, IN 46617
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, South Bend, IN 46617
| | - Zachary D Schultz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
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11
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Xiao L, Wang C, Dai C, Littlepage LE, Li J, Schultz ZD. Untargeted Tumor Metabolomics with Liquid Chromatography–Surface‐Enhanced Raman Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lifu Xiao
- Department of Chemistry and BiochemistryThe Ohio State University Columbus OH 43210 USA
| | - Chuanqi Wang
- Department of Applied and Computational Mathematics and StatisticsUniversity of Notre Dame Notre Dame IN 46556 USA
- Harper Cancer Research Institute South Bend IN 46617 USA
| | - Chen Dai
- Department of Chemistry and BiochemistryUniversity of Notre Dame Notre Dame IN 46556 USA
- Harper Cancer Research Institute South Bend IN 46617 USA
| | - Laurie E. Littlepage
- Department of Chemistry and BiochemistryUniversity of Notre Dame Notre Dame IN 46556 USA
- Harper Cancer Research Institute South Bend IN 46617 USA
| | - Jun Li
- Department of Applied and Computational Mathematics and StatisticsUniversity of Notre Dame Notre Dame IN 46556 USA
- Harper Cancer Research Institute South Bend IN 46617 USA
| | - Zachary D. Schultz
- Department of Chemistry and BiochemistryThe Ohio State University Columbus OH 43210 USA
- Comprehensive Cancer CenterThe Ohio State University Columbus OH 43210 USA
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12
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Current trends in isotope‐coded derivatization liquid chromatographic‐mass spectrometric analyses with special emphasis on their biomedical application. Biomed Chromatogr 2020; 34:e4756. [DOI: 10.1002/bmc.4756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
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13
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Schwaiger M, Schoeny H, El Abiead Y, Hermann G, Rampler E, Koellensperger G. Merging metabolomics and lipidomics into one analytical run. Analyst 2019; 144:220-229. [PMID: 30411762 DOI: 10.1039/c8an01219a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel integrated metabolomics/lipidomics workflow is introduced enabling high coverage of polar metabolites and non-polar lipids within one analytical run. Dual HILIC and RP chromatography were combined to high-resolution mass spectrometry. As a major advantage, only one data file per sample was obtained by fully automated simultaneous analysis of two extracts per sample. Hence, the unprecedented high coverage without compromise on analytical throughput was not only obtained by the orthogonality of the chromatographic separations, but also by the implementation of dedicated sample preparation procedures resulting in optimum extraction efficiency for both sub-omes. Thus, the method addressed completely hydrophilic sugars and organic acids next to water-insoluble triglycerides. As for the timing of the dual chromatography setup, HILIC and RP separation were performed consecutively. However, re-equilibration of the HILIC column during elution of RP compounds and vice versa reduced the overall analysis time by one third to 32 min. Application to the Standard Reference Material SRM 1950 - Metabolites in Frozen Human Plasma resulted in >100 metabolite and >380 lipid identifications based on accurate mass implementing fast polarity switching and acquiring data dependent MS2 spectra with the use of automated exclusion lists. Targeted quantification based on external calibrations and 13C labeled yeast internal standards was successfully accomplished for 59 metabolites. Moreover, the potential for lipid quantification was shown integrating non-endogenous lipids as internal standards. In human plasma, concentrations ranging over 4 orders of magnitude (low nM to high μM) were assessed.
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Affiliation(s)
- Michaela Schwaiger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and ISOtopic solutions, Waehringerstr. 38, 1090 Vienna, Austria
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiology, Althanstraße 14, 1090 Vienna, Austria
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14
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Abstract
Nano liquid chromatography (nanoLC), with columns having an inner diameter (ID) of ≤100 μm, can provide enhanced sensitivity and enable analysis of limited samples.
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Affiliation(s)
- Steven Ray Wilson
- Department of Chemistry
- University of Oslo
- Oslo
- Norway
- Hybrid Technology Hub-Centre of Excellence
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15
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Huang T, Armbruster MR, Coulton JB, Edwards JL. Chemical Tagging in Mass Spectrometry for Systems Biology. Anal Chem 2018; 91:109-125. [DOI: 10.1021/acs.analchem.8b04951] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Michael R. Armbruster
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - John B. Coulton
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - James L. Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
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16
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Vuckovic D. Improving metabolome coverage and data quality: advancing metabolomics and lipidomics for biomarker discovery. Chem Commun (Camb) 2018; 54:6728-6749. [PMID: 29888773 DOI: 10.1039/c8cc02592d] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This Feature Article highlights some of the key challenges within the field of metabolomics and examines what role separation and analytical sciences can play to improve the use of metabolomics in biomarker discovery and personalized medicine. Recent progress in four key areas is highlighted: (i) improving metabolite coverage, (ii) developing accurate methods for unstable metabolites including in vivo global metabolomics methods, (iii) advancing inter-laboratory studies and reference materials and (iv) improving data quality, standardization and quality control of metabolomics studies.
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Affiliation(s)
- Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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17
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Xie B, Wang Y, Jones DR, Dey KK, Wang X, Li Y, Cho JH, Shaw TI, Tan H, Peng J. Isotope Labeling-Assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling. Anal Chem 2018; 90:8538-8545. [PMID: 29883117 DOI: 10.1021/acs.analchem.8b01591] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High throughput untargeted metabolomics usually relies on complementary liquid chromatography-mass spectrometry (LC-MS) methods to expand the coverage of diverse metabolites, but the integration of those methods is not fully characterized. We systematically investigated the performance of hydrophilic interaction liquid chromatography (HILIC)-MS and nanoflow reverse-phase liquid chromatography (nRPLC)-MS under 8 LC-MS settings, varying stationary phases (HILIC and C18), mobile phases (acidic and basic pH), and MS ionization modes (positive and negative). Whereas nRPLC-MS optimization was previously reported, we found in HILIC-MS (2.1 mm × 150 mm) that the optimal performance was achieved in a 90 min gradient with 100 μL/min flow rate by loading metabolite extracts from 2 mg of cell/tissue samples. Since peak features were highly compromised by contaminants, we used stable isotope labeled yeast to enhance formula identification for comparing different LC-MS conditions. The 8 LC-MS settings enabled the detection of a total of 1050 formulas, among which 78%, 73%, and 62% formulas were recovered by the best combination of 4, 3, and 2 LC-MS settings, respectively. Moreover, these yeast samples were harvested in the presence or absence of nitrogen starvation, enabling quantitative comparisons of altered formulas and metabolite structures, followed by validation with selected synthetic metabolites. The results revealed that nitrogen starvation downregulated amino acid components but upregulated uridine-related metabolism. In summary, this study introduces a thorough evaluation of hydrophilicity and hydrophobicity based LC-MS and provides information for selecting complementary settings to balance throughput and efficiency during metabolomics experiments.
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18
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A review of nanoscale LC-ESI for metabolomics and its potential to enhance the metabolome coverage. Talanta 2018; 182:380-390. [PMID: 29501168 DOI: 10.1016/j.talanta.2018.01.084] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/22/2022]
Abstract
Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) platforms are widely used to perform high throughput untargeted profiling of biological samples for metabolomics-based approaches. However, these LC-ESI platforms usually favour the detection of metabolites present at relatively high concentrations because of analytical limitations such as ion suppression, thus reducing overall sensitivity. To counter this issue of sensitivity, the latest in terms of analytical platforms can be adopted to enable a greater portion of the metabolome to be analysed in a single analytical run. Here, nanoflow liquid chromatography-nanoelectrospray ionisation (nLC-nESI), which has previously been utilised successfully in proteomics, is explored for use in metabolomic and exposomic research. As a discovery based field, the markedly increased sensitivity of these nLC-nESI platforms offer the potential to uncover the roles played by low abundant signalling metabolites (e.g. steroids, eicosanoids) in health and disease studies, and would also enable an improvement in the detection of xenobiotics present at trace levels in biological matrices to better characterise the chemical exposome. This review aims to give an insight into the advantages associated with nLC-nESI for metabolomics-based approaches. Initially we detail the source of improved sensitivity prior to reviewing the available approaches to achieving nanoflow rates and nanospray ionisation for metabolomics. The robustness of nLC-nESI platforms was then assessed using the literature available from a metabolomic viewpoint. We also discuss the challenging point of sample preparation which needs to be addressed to fully enjoy the benefits of these nLC-nESI platforms. Finally, we assess metabolomic analysis utilising nano scale platforms and look ahead to the future of metabolomics using these new highly sensitive platforms.
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Blum BC, Mousavi F, Emili A. Single-platform ‘multi-omic’ profiling: unified mass spectrometry and computational workflows for integrative proteomics–metabolomics analysis. Mol Omics 2018; 14:307-319. [DOI: 10.1039/c8mo00136g] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Advances in instrumentation and analysis tools are permitting evermore comprehensive interrogation of diverse biomolecules and allowing investigators to move from linear signaling cascades to network models, which more accurately reflect the molecular basis of biological systems and processes.
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Affiliation(s)
- Benjamin C. Blum
- Center for Network Systems Biology
- Boston University School of Medicine
- Boston
- USA
- Department of Biochemistry
| | - Fatemeh Mousavi
- Donnelly Centre
- Department of Molecular Genetics
- University of Toronto
- Toronto
- Canada
| | - Andrew Emili
- Center for Network Systems Biology
- Boston University School of Medicine
- Boston
- USA
- Department of Biochemistry
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20
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Luo X, Li L. Metabolomics of Small Numbers of Cells: Metabolomic Profiling of 100, 1000, and 10000 Human Breast Cancer Cells. Anal Chem 2017; 89:11664-11671. [DOI: 10.1021/acs.analchem.7b03100] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xian Luo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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21
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Zhang S, Shi J, Shan C, Huang C, Wu Y, Ding R, Xue Y, Liu W, Zhou Q, Zhao Y, Xu P, Gao X. Stable isotope N -phosphoryl amino acids labeling for quantitative profiling of amine-containing metabolites using liquid chromatography mass spectrometry. Anal Chim Acta 2017; 978:24-34. [DOI: 10.1016/j.aca.2017.04.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/10/2017] [Accepted: 04/20/2017] [Indexed: 12/16/2022]
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Hao L, Johnson J, Lietz CB, Buchberger A, Frost D, Kao WJ, Li L. Mass Defect-Based N,N-Dimethyl Leucine Labels for Quantitative Proteomics and Amine Metabolomics of Pancreatic Cancer Cells. Anal Chem 2017; 89:1138-1146. [PMID: 28194987 DOI: 10.1021/acs.analchem.6b03482] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mass spectrometry-based stable isotope labeling has become a key technology for protein and small-molecule analyses. We developed a multiplexed quantification method for simultaneous proteomics and amine metabolomics analyses via nano reversed-phase liquid chromatography-tandem mass spectrometry (nanoRPLC-MS/MS), called mass defect-based N,N-dimethyl leucine (mdDiLeu) labeling. The duplex mdDiLeu reagents were custom-synthesized with a mass difference of 20.5 mDa, arising from the subtle variation in nuclear binding energy between the two DiLeu isotopologues. Optimal MS resolving powers were determined to be 240K for labeled peptides and 120K for labeled metabolites on the Orbitrap Fusion Lumos instrument. The mdDiLeu labeling does not suffer from precursor interference and dynamic range compression, providing excellent accuracy for MS1-centric quantification. Quantitative information is only revealed at high MS resolution without increasing spectrum complexity and overlapping isotope distribution. Chromatographic performance of polar metabolites was dramatically improved by mdDiLeu labeling with modified hydrophobicity, enhanced ionization efficiency, and picomole levels of detection limits. Paralleled proteomics and amine metabolomics analyses using mdDiLeu were systematically evaluated and then applied to pancreatic cancer cells.
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Affiliation(s)
- Ling Hao
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Christopher B Lietz
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Amanda Buchberger
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dustin Frost
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - W John Kao
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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Huan T, Xian JW, Leung WN, Li L, Chan CW. Cerebrospinal Fluid Metabolomics After Natural Product Treatment in an Experimental Model of Cerebral Ischemia. ACTA ACUST UNITED AC 2016; 20:670-680. [DOI: 10.1089/omi.2016.0112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tao Huan
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jia Wen Xian
- School of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Wing Nang Leung
- School of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Chun Wai Chan
- School of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Isotope-coded ESI-enhancing derivatization reagents for differential analysis, quantification and profiling of metabolites in biological samples by LC/MS: A review. J Pharm Biomed Anal 2016; 130:181-193. [DOI: 10.1016/j.jpba.2016.04.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/20/2016] [Accepted: 04/20/2016] [Indexed: 12/15/2022]
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Hooton K, Han W, Li L. Comprehensive and Quantitative Profiling of the Human Sweat Submetabolome Using High-Performance Chemical Isotope Labeling LC–MS. Anal Chem 2016; 88:7378-86. [DOI: 10.1021/acs.analchem.6b01930] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kevin Hooton
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wei Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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