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Drakopoulou SK, Kritikou AS, Baessmann C, Thomaidis NS. Untargeted 4D-metabolomics using Trapped Ion Mobility combined with LC-HRMS in extra virgin olive oil adulteration study with lower-quality olive oils. Food Chem 2024; 434:137410. [PMID: 37708573 DOI: 10.1016/j.foodchem.2023.137410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 08/28/2023] [Accepted: 09/03/2023] [Indexed: 09/16/2023]
Abstract
Metabolomics is widely established in the field of food authenticity to address demanding issues, such as adulteration cases. Trapped ion mobility spectrometry (TIMS) coupled to liquid chromatography (LC) and high-resolution mass spectrometry (HRMS) provides an additional analytical dimension, introducing mobility-enhanced metabolomics in four dimensions (4D). In the present work, the potential of LC-TIMS-HRMS as a reliable analytical platform for authenticity studies is being explored, applied in extra virgin olive oil (EVOO) adulteration study. An integrated untargeted 4D-metabolomics approach is being implemented to investigate adulteration, with refined olive oils (ROOs) and olive pomace oils (OPOs) set as adulterants. Robust prediction models are built, successfully discriminating authentic EVOOs from adulterated ones and highlighting markers in each group. Noteworthy outcomes are retrieved regarding TIMS added value in LC-HRMS workflows, resulting in a significant increase of metabolic coverage, while, thanks to platform's enhanced sensitivity, detection of adulteration is being achieved down to 1%.
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Affiliation(s)
- Sofia K Drakopoulou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Anastasia S Kritikou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | | | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece.
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2
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Heuckeroth S, Behrens A, Wolf C, Fütterer A, Nordhorn ID, Kronenberg K, Brungs C, Korf A, Richter H, Jeibmann A, Karst U, Schmid R. On-tissue dataset-dependent MALDI-TIMS-MS 2 bioimaging. Nat Commun 2023; 14:7495. [PMID: 37980348 PMCID: PMC10657435 DOI: 10.1038/s41467-023-43298-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
Trapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS2) impedes confident compound annotation in spatial metabolomics. Here, we describe spatial ion mobility-scheduled exhaustive fragmentation (SIMSEF), a dataset-dependent acquisition strategy that augments TIMS-MS imaging datasets with MS2 spectra. The fragmentation experiments are systematically distributed across the sample and scheduled for multiple collision energies per precursor ion. Extendable data processing and evaluation workflows are implemented into the open source software MZmine. The workflow and annotation capabilities are demonstrated on rat brain tissue thin sections, measured by matrix-assisted laser desorption/ionisation (MALDI)-TIMS-MS, where SIMSEF enables on-tissue compound annotation through spectral library matching and rule-based lipid annotation within MZmine and maps the (un)known chemical space by molecular networking. The SIMSEF algorithm and data analysis pipelines are open source and modular to provide a community resource.
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Affiliation(s)
- Steffen Heuckeroth
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | | | - Carina Wolf
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | | | - Ilona D Nordhorn
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Katharina Kronenberg
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Corinna Brungs
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ansgar Korf
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Henning Richter
- Clinic for Diagnostic Imaging, Diagnostic Imaging Research Unit (DIRU), University of Zurich, Zürich, Switzerland
| | - Astrid Jeibmann
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Robin Schmid
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
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3
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Moses T, Burgess K. Right in two: capabilities of ion mobility spectrometry for untargeted metabolomics. Front Mol Biosci 2023; 10:1230282. [PMID: 37602325 PMCID: PMC10436490 DOI: 10.3389/fmolb.2023.1230282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
This mini review focuses on the opportunities provided by current and emerging separation techniques for mass spectrometry metabolomics. The purpose of separation technologies in metabolomics is primarily to reduce complexity of the heterogeneous systems studied, and to provide concentration enrichment by increasing sensitivity towards the quantification of low abundance metabolites. For this reason, a wide variety of separation systems, from column chemistries to solvent compositions and multidimensional separations, have been applied in the field. Multidimensional separations are a common method in both proteomics applications and gas chromatography mass spectrometry, allowing orthogonal separations to further reduce analytical complexity and expand peak capacity. These applications contribute to exponential increases in run times concomitant with first dimension fractionation followed by second dimension separations. Multidimensional liquid chromatography to increase peak capacity in metabolomics, when compared to the potential of running additional samples or replicates and increasing statistical confidence, mean that uptake of these methods has been minimal. In contrast, in the last 15 years there have been significant advances in the resolution and sensitivity of ion mobility spectrometry, to the point where high-resolution separation of analytes based on their collision cross section approaches chromatographic separation, with minimal loss in sensitivity. Additionally, ion mobility separations can be performed on a chromatographic timescale with little reduction in instrument duty cycle. In this review, we compare ion mobility separation to liquid chromatographic separation, highlight the history of the use of ion mobility separations in metabolomics, outline the current state-of-the-art in the field, and discuss the future outlook of the technology. "Where there is one, you're bound to divide it. Right in two", James Maynard Keenan.
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Affiliation(s)
- Tessa Moses
- EdinOmics, RRID:SCR_021838, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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4
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Li X, Wang H, Jiang M, Ding M, Xu X, Xu B, Zou Y, Yu Y, Yang W. Collision Cross Section Prediction Based on Machine Learning. Molecules 2023; 28:molecules28104050. [PMID: 37241791 DOI: 10.3390/molecules28104050] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Ion mobility-mass spectrometry (IM-MS) is a powerful separation technique providing an additional dimension of separation to support the enhanced separation and characterization of complex components from the tissue metabolome and medicinal herbs. The integration of machine learning (ML) with IM-MS can overcome the barrier to the lack of reference standards, promoting the creation of a large number of proprietary collision cross section (CCS) databases, which help to achieve the rapid, comprehensive, and accurate characterization of the contained chemical components. In this review, advances in CCS prediction using ML in the past 2 decades are summarized. The advantages of ion mobility-mass spectrometers and the commercially available ion mobility technologies with different principles (e.g., time dispersive, confinement and selective release, and space dispersive) are introduced and compared. The general procedures involved in CCS prediction based on ML (acquisition and optimization of the independent and dependent variables, model construction and evaluation, etc.) are highlighted. In addition, quantum chemistry, molecular dynamics, and CCS theoretical calculations are also described. Finally, the applications of CCS prediction in metabolomics, natural products, foods, and the other research fields are reflected.
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Affiliation(s)
- Xiaohang Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Hongda Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Meiting Jiang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Mengxiang Ding
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Xiaoyan Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Bei Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Yadan Zou
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Yuetong Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Wenzhi Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
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Amer B, Deshpande RR, Bird SS. Simultaneous Quantitation and Discovery (SQUAD) Analysis: Combining the Best of Targeted and Untargeted Mass Spectrometry-Based Metabolomics. Metabolites 2023; 13:metabo13050648. [PMID: 37233689 DOI: 10.3390/metabo13050648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Untargeted and targeted approaches are the traditional metabolomics workflows acquired for a wider understanding of the metabolome under focus. Both approaches have their strengths and weaknesses. The untargeted, for example, is maximizing the detection and accurate identification of thousands of metabolites, while the targeted is maximizing the linear dynamic range and quantification sensitivity. These workflows, however, are acquired separately, so researchers compromise either a low-accuracy overview of total molecular changes (i.e., untargeted analysis) or a detailed yet blinkered snapshot of a selected group of metabolites (i.e., targeted analysis) by selecting one of the workflows over the other. In this review, we present a novel single injection simultaneous quantitation and discovery (SQUAD) metabolomics that combines targeted and untargeted workflows. It is used to identify and accurately quantify a targeted set of metabolites. It also allows data retro-mining to look for global metabolic changes that were not part of the original focus. This offers a way to strike the balance between targeted and untargeted approaches in one single experiment and address the two approaches' limitations. This simultaneous acquisition of hypothesis-led and discovery-led datasets allows scientists to gain more knowledge about biological systems in a single experiment.
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Affiliation(s)
- Bashar Amer
- Thermo Fisher Scientific, San Jose, 95134 CA, USA
| | | | - Susan S Bird
- Thermo Fisher Scientific, San Jose, 95134 CA, USA
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6
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May JC, McLean JA. Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations. Metabolomics 2022; 18:104. [PMID: 36472678 DOI: 10.1007/s11306-022-01961-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Ion mobility (IM) separation capabilities are now widely available to researchers through several commercial vendors and are now being adopted into many metabolomics workflows. The added peak capacity that ion mobility offers with minimal compromise to other analytical figures-of-merit has provided real benefits to sensitivity and structural selectivity and have allowed more specific metabolite annotations to be assigned in untargeted workflows. One of the greatest promises of contemporary IM-enabled instrumentation is the capability of operating multiple analytical dimensions inline with minimal sample volumes, which has the potential to address many grand challenges currently faced in the omics fields. However, comprehensive operation of multidimensional mass spectrometry comes with its own inherent challenges that, beyond operational complexity, may not be immediately obvious to practitioners of these techniques. AIM OF REVIEW In this review, we outline the strengths and considerations for incorporating IM analysis in metabolomics workflows and provide a critical but forward-looking perspective on the contemporary challenges and prospects associated with interpreting IM data into chemical knowledge. KEY SCIENTIFIC CONCEPTS OF REVIEW We outline a strategy for unifying IM-derived collision cross section (CCS) measurements obtained from different IM techniques and discuss the emerging field of high resolution ion mobility (HRIM) that is poised to address many of the contemporary challenges associated with ion mobility metabolomics. Whereas the LC step limits the throughput of comprehensive LC-IM-MS, the higher peak capacity of HRIM can allow fast LC gradients or rapid sample cleanup via solid-phase extraction (SPE) to be utilized, significantly improving the sample throughput.
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Affiliation(s)
- Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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7
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Hu C, Zhang Y, Zhou Y, Xiang YJY, Liu ZF, Wang ZH, Feng XS. Tetrodotoxin and Its Analogues in Food: Recent Updates on Sample Preparation and Analytical Methods Since 2012. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12249-12269. [PMID: 36153990 DOI: 10.1021/acs.jafc.2c04106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Tetrodotoxin (TTX), found in various organisms including pufferfish, is an extremely potent marine toxin responsible for numerous food poisoning accidents. Due to its serious toxicity and public health threat, detecting TTX and its analogues in diverse food matrices with a simple, fast, efficient method has become a worldwide concern. This review summarizes the advances in sample preparation and analytical methods for the determination of TTX and its analogues, focusing on the latest development over the past five years. Current state-of-the-art technologies, such as solid-phase microextraction, online technology, novel injection technology, two-dimensional liquid chromatography, high-resolution mass spectrometry, newly developed lateral flow immunochromatographic strips, immunosensors, dual-mode aptasensors, and nanomaterials-based approaches, are thoroughly discussed. The advantages and limitations of different techniques, critical comments, and future perspectives are also proposed. This review is expected to provide rewarding insights to the future development and broad application of pretreatment and detection methods for TTX and its analogues.
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Affiliation(s)
- Cong Hu
- School of Pharmacy, China Medical University, Shenyang 110122, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yuan Zhang
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Yu Zhou
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang-Jia-Yi Xiang
- Department of Pharmaceutical Analysis, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Zhi-Fei Liu
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Zhi-Hong Wang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Xue-Song Feng
- School of Pharmacy, China Medical University, Shenyang 110122, China
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9
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González-Domínguez R, Sayago A, Santos-Martín M, Fernández-Recamales Á. High-Throughput Method for Wide-Coverage and Quantitative Phenolic Fingerprinting in Plant-Origin Foods and Urine Samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7796-7804. [PMID: 35703393 PMCID: PMC10550202 DOI: 10.1021/acs.jafc.2c01453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The use of mass spectrometry is currently widespread in polyphenol research because of its sensitivity and selectivity, but its usual high cost, reduced robustness, and nonavailability in many analytical laboratories considerably hinder its routine implementation. Herein, we describe the optimization and validation of a high-throughput, wide-coverage, and robust metabolomics method based on reversed-phase ultra-high-performance liquid chromatography with diode array detection for the identification and quantification of 69 phenolic compounds and related metabolites covering a broad chemical space of the characteristic secondary metabolome of plant foods. The method was satisfactorily validated following the Food and Drug Administration guidelines in terms of linearity (4-5 orders of magnitude), limits of quantification (0.007-3.6 mg L-1), matrix effect (60.5-124.4%), accuracy (63.4-126.7%), intraday precision (0.1-9.6%), interday precision (0.6-13.7%), specificity, and carryover. Then, it was successfully applied to characterize the phenolic fingerprints of diverse food products (i.e., olive oil, red wine, strawberry) and biological samples (i.e., urine), enabling not only the detection of many of the target compounds but also the semi-quantification of other phenolic metabolites tentatively identified based on their characteristic absorption spectra. Therefore, this method represents one step further toward time-efficient and low-cost polyphenol fingerprinting, with suitable applicability in the food industry to ensure food quality, safety, authenticity, and traceability.
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Affiliation(s)
- Raúl González-Domínguez
- Agrifood
Laboratory, Faculty of Experimental Sciences, University of Huelva, 21007 Huelva, Spain
- International
Campus of Excellence CeiA3, University of
Huelva, 21007 Huelva, Spain
| | - Ana Sayago
- Agrifood
Laboratory, Faculty of Experimental Sciences, University of Huelva, 21007 Huelva, Spain
- International
Campus of Excellence CeiA3, University of
Huelva, 21007 Huelva, Spain
| | - María Santos-Martín
- Agrifood
Laboratory, Faculty of Experimental Sciences, University of Huelva, 21007 Huelva, Spain
- International
Campus of Excellence CeiA3, University of
Huelva, 21007 Huelva, Spain
| | - Ángeles Fernández-Recamales
- Agrifood
Laboratory, Faculty of Experimental Sciences, University of Huelva, 21007 Huelva, Spain
- International
Campus of Excellence CeiA3, University of
Huelva, 21007 Huelva, Spain
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Quiles C, Viera I, Roca M. Multiomics Approach To Decipher the Origin of Chlorophyll Content in Virgin Olive Oil. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3807-3817. [PMID: 35290057 PMCID: PMC8972264 DOI: 10.1021/acs.jafc.2c00031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The color of virgin olive oils, ranging from intense green to brown-yellow, is one of the main selection factors for consumers and a quality criterion in specific legislations. Such coloration is due to their chlorophyll content and depends on the composition of the olive fruit. Through analytical chemistry (HPLC-hrMSn), biochemistry (enzymatic activity), and molecular biology (qRT-PCR) approaches, we have analyzed the origin of the differences in the chlorophyll content among several varieties of olive fruit throughout their ripening process. The higher chlorophyll biosynthetic capacity in olive fruits is due to the enzyme protochlorophyllide reductase, whereas chlorophyll degradation is accomplished through the stay-green and pheophytinase pathways. For the first time, the implication of chlorophyll dephytylase during the turnover of chlorophylls in fruit is shown to be responsible for the exclusive accumulation of dephytylated chlorophyll in Arbequina fruit. The multiomics results excluded the in vivo participation of chlorophyllase in chlorophyll degradation in olive fruits.
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Affiliation(s)
| | | | - María Roca
- . Tel.: +00 34 954.61.15.50. Fax: +00 34 954.61.67.90
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