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Mansoor S, Hamid S, Tuan TT, Park JE, Chung YS. Advance computational tools for multiomics data learning. Biotechnol Adv 2024; 77:108447. [PMID: 39251098 DOI: 10.1016/j.biotechadv.2024.108447] [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: 05/19/2024] [Revised: 09/01/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
The burgeoning field of bioinformatics has seen a surge in computational tools tailored for omics data analysis driven by the heterogeneous and high-dimensional nature of omics data. In biomedical and plant science research multi-omics data has become pivotal for predictive analytics in the era of big data necessitating sophisticated computational methodologies. This review explores a diverse array of computational approaches which play crucial role in processing, normalizing, integrating, and analyzing omics data. Notable methods such similarity-based methods, network-based approaches, correlation-based methods, Bayesian methods, fusion-based methods and multivariate techniques among others are discussed in detail, each offering unique functionalities to address the complexities of multi-omics data. Furthermore, this review underscores the significance of computational tools in advancing our understanding of data and their transformative impact on research.
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Affiliation(s)
- Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea
| | - Saira Hamid
- Watson Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Thai Thanh Tuan
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea; Multimedia Communications Laboratory, University of Information Technology, Ho Chi Minh city 70000, Vietnam; Multimedia Communications Laboratory, Vietnam National University, Ho Chi Minh city 70000, Vietnam
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju, Jeju-do, Republic of Korea.
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea.
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Sun X, Song Z, Tang Z, Yu J, Fan X, Yang Y, Yuan S, Chen Q. Effects of different post-harvest processing methods on changes in the active ingredients of licorice based on LC-MS and plant metabolomics. PHYTOCHEMICAL ANALYSIS : PCA 2024. [PMID: 38989561 DOI: 10.1002/pca.3419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
INTRODUCTION Licorice, the dried roots and rhizomes of the Glycyrrhiza uralensis Fisch., holds a prominent status in various formulations within the realm of Chinese medicinal practices. The traditional processing methods of licorice hinder quality assurance, thus prompting Chinese medicine researchers to focus on the fresh processing methods to enhancing processing efficiency and quality. OBJECTIVE This study aimed to identify the differential compounds of licorice between traditional and fresh processing methods and provide a scientific basis for the fresh processing of licorice and for further research on the processing mechanism. METHODOLOGY A methodology integrating ultra-performance liquid chromatography with quadrupole-time-of-flight tandem mass spectrometry combined with multivariate statistical analysis was employed to characterize the differential compounds present in licorice between traditional processing and fresh processing. RESULTS The results derived from principal component analysis and heat map analyses underscored significant differences in the content of bioactive compounds between the two processing methods. By applying conditions of VIP > 1.5 and p < 0.05, a total of 38 differential compounds were identified through t tests, and the transformation mechanisms of select compounds were illustrated. CONCLUSION The adoption of fresh processing techniques not only improved processing efficiency but also significantly enhanced the preservation of bioactive compounds within licorice. This research has established a rapid and efficient analytical method for the identification of differential compounds present in differently processed licorice products.
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Affiliation(s)
- Xiaoxu Sun
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Zhongxing Song
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Zhishu Tang
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingao Yu
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Xiuhe Fan
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yuangui Yang
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Shuhui Yuan
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Qiang Chen
- Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, China
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3
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Eshawu AB, Ghalsasi VV. Metabolomics of natural samples: A tutorial review on the latest technologies. J Sep Sci 2024; 47:e2300588. [PMID: 37942863 DOI: 10.1002/jssc.202300588] [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: 08/13/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 11/10/2023]
Abstract
Metabolomics is the study of metabolites present in a living system. It is a rapidly growing field aimed at discovering novel compounds, studying biological processes, diagnosing diseases, and ensuring the quality of food products. Recently, the analysis of natural samples has become important to explore novel bioactive compounds and to study how environment and genetics affect living systems. Various metabolomics techniques, databases, and data analysis tools are available for natural sample metabolomics. However, choosing the right method can be a daunting exercise because natural samples are heterogeneous and require untargeted approaches. This tutorial review aims to compile the latest technologies to guide an early-career scientist on natural sample metabolomics. First, different extraction methods and their pros and cons are reviewed. Second, currently available metabolomics databases and data analysis tools are summarized. Next, recent research on metabolomics of milk, honey, and microbial samples is reviewed. Finally, after reviewing the latest trends in technologies, a checklist is presented to guide an early-career researcher on how to design a metabolomics project. In conclusion, this review is a comprehensive resource for a researcher planning to conduct their first metabolomics analysis. It is also useful for experienced researchers to update themselves on the latest trends in metabolomics.
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Affiliation(s)
- Ali Baba Eshawu
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Vihang Vivek Ghalsasi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
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Rodeiro J, Vidaña-Vila E, Navarro J, Mallol R. CloMet: A Novel Open-Source and Modular Software Platform That Connects Established Metabolomics Repositories and Data Analysis Resources. J Proteome Res 2023; 22:2540-2547. [PMID: 37428859 PMCID: PMC10857572 DOI: 10.1021/acs.jproteome.2c00602] [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: 09/29/2022] [Indexed: 07/12/2023]
Abstract
The field of metabolomics has witnessed the development of hundreds of computational tools, but only a few have become cornerstones of this field. While MetaboLights and Metabolomics Workbench are two well-established data repositories for metabolomics data sets, Workflows4Metabolomics and MetaboAnalyst are two well-established web-based data analysis platforms for metabolomics. Yet, the raw data stored in the aforementioned repositories lack standardization in terms of the file system format used to store the associated acquisition files. Consequently, it is not straightforward to reuse available data sets as input data in the above-mentioned data analysis resources, especially for non-expert users. This paper presents CloMet, a novel open-source modular software platform that contributes to standardization, reusability, and reproducibility in the metabolomics field. CloMet, which is available through a Docker file, converts raw and NMR-based metabolomics data from MetaboLights and Metabolomics Workbench to a file format that can be used directly either in MetaboAnalyst or in Workflows4Metabolomics. We validated both CloMet and the output data using data sets from these repositories. Overall, CloMet fills the gap between well-established data repositories and web-based statistical platforms and contributes to the consolidation of a data-driven perspective of the metabolomics field by leveraging and connecting existing data and resources.
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Affiliation(s)
- Jordi Rodeiro
- Human
Environment Research, La Salle - Universitat
Ramon Llull, 08022 Barcelona, Spain
| | - Ester Vidaña-Vila
- Human
Environment Research, La Salle - Universitat
Ramon Llull, 08022 Barcelona, Spain
| | - Joan Navarro
- Research
Group on Smart Society, La Salle - Universitat
Ramon Llull, 08022 Barcelona, Spain
| | - Roger Mallol
- Human
Environment Research, La Salle - Universitat
Ramon Llull, 08022 Barcelona, Spain
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5
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Garcia-Perez P, Cassani L, Garcia-Oliveira P, Xiao J, Simal-Gandara J, Prieto MA, Lucini L. Algal nutraceuticals: A perspective on metabolic diversity, current food applications, and prospects in the field of metabolomics. Food Chem 2023; 409:135295. [PMID: 36603477 DOI: 10.1016/j.foodchem.2022.135295] [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: 09/20/2022] [Revised: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The current consumers' demand for food naturalness is urging the search for new functional foods of natural origin with enhanced health-promoting properties. In this sense, algae constitute an underexplored biological source of nutraceuticals that can be used to fortify food products. Both marine macroalgae (or seaweeds) and microalgae exhibit a myriad of chemical constituents with associated features as a result of their primary and secondary metabolism. Thus, primary metabolites, especially polysaccharides and phycobiliproteins, present interesting properties to improve the rheological and nutritional properties of food matrices, whereas secondary metabolites, such as polyphenols and xanthophylls, may provide interesting bioactivities, including antioxidant or cytotoxic effects. Due to the interest in algae as a source of nutraceuticals by the food and related industries, novel strategies should be undertaken to add value to their derived functional components. As a result, metabolomics is considered a high throughput technology to get insight into the full metabolic profile of biological samples, and it opens a wide perspective in the study of algae metabolism, whose knowledge is still little explored. This review focuses on algae metabolism and its applications in the food industry, paying attention to the promising metabolomic approaches to be developed aiming at the functional characterization of these organisms.
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Affiliation(s)
- Pascual Garcia-Perez
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - Lucia Cassani
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Centro de Investigação de Montanha (CIMO-IPB), Campus de Santa Apolónia, Bragança, Portugal
| | - Paula Garcia-Oliveira
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Centro de Investigação de Montanha (CIMO-IPB), Campus de Santa Apolónia, Bragança, Portugal
| | - Jianbo Xiao
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain
| | - Miguel A Prieto
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Centro de Investigação de Montanha (CIMO-IPB), Campus de Santa Apolónia, Bragança, Portugal
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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Parker EJ, Billane KC, Austen N, Cotton A, George RM, Hopkins D, Lake JA, Pitman JK, Prout JN, Walker HJ, Williams A, Cameron DD. Untangling the Complexities of Processing and Analysis for Untargeted LC-MS Data Using Open-Source Tools. Metabolites 2023; 13:metabo13040463. [PMID: 37110122 PMCID: PMC10142740 DOI: 10.3390/metabo13040463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Untargeted metabolomics is a powerful tool for measuring and understanding complex biological chemistries. However, employment, bioinformatics and downstream analysis of mass spectrometry (MS) data can be daunting for inexperienced users. Numerous open-source and free-to-use data processing and analysis tools exist for various untargeted MS approaches, including liquid chromatography (LC), but choosing the 'correct' pipeline isn't straight-forward. This tutorial, in conjunction with a user-friendly online guide presents a workflow for connecting these tools to process, analyse and annotate various untargeted MS datasets. The workflow is intended to guide exploratory analysis in order to inform decision-making regarding costly and time-consuming downstream targeted MS approaches. We provide practical advice concerning experimental design, organisation of data and downstream analysis, and offer details on sharing and storing valuable MS data for posterity. The workflow is editable and modular, allowing flexibility for updated/changing methodologies and increased clarity and detail as user participation becomes more common. Hence, the authors welcome contributions and improvements to the workflow via the online repository. We believe that this workflow will streamline and condense complex mass-spectrometry approaches into easier, more manageable, analyses thereby generating opportunities for researchers previously discouraged by inaccessible and overly complicated software.
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Affiliation(s)
| | - Kathryn C Billane
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Nichola Austen
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Anne Cotton
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Rachel M George
- biOMICS Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - David Hopkins
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Janice A Lake
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK
| | - James K Pitman
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - James N Prout
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Heather J Walker
- biOMICS Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Williams
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Duncan D Cameron
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK
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Wang W, Ma LH, Maletic-Savatic M, Liu Z. NMRQNet: a deep learning approach for automatic identification and quantification of metabolites using Nuclear Magnetic Resonance (NMR) in human plasma samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530642. [PMID: 36909516 PMCID: PMC10002723 DOI: 10.1101/2023.03.01.530642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Nuclear Magnetic Resonance is a powerful platform that reveals the metabolomics profiles within biofluids or tissues and contributes to personalized treatments in medical practice. However, data volume and complexity hinder the exploration of NMR spectra. Besides, the lack of fast and accurate computational tools that can handle the automatic identification and quantification of essential metabolites from NMR spectra also slows the wide application of these techniques in clinical. We present NMRQNet, a deep-learning-based pipeline for automatic identification and quantification of dominant metabolite candidates within human plasma samples. The estimated relative concentrations could be further applied in statistical analysis to extract the potential biomarkers. We evaluate our method on multiple plasma samples, including species from mice to humans, curated using three anticoagulants, covering healthy and patient conditions in neurological disorder disease, greatly expanding the metabolomics analytical space in plasma. NMRQNet accurately reconstructed the original spectra and obtained significantly better quantification results than the earlier computational methods. Besides, NMRQNet also proposed relevant metabolites biomarkers that could potentially explain the risk factors associated with the condition. NMRQNet, with improved prediction performance, highlights the limitations in the existing approaches and has shown strong application potential for future metabolomics disease studies using plasma samples.
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Affiliation(s)
- Wanli Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Graduate Program of Quantitative & Computational Biosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Li-Hua Ma
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mirjana Maletic-Savatic
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
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8
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Howell-Bray T, Byrne L. The effect of prions on cellular metabolism: The metabolic impact of the [RNQ +] prion and potential role of native Rnq1p. RESEARCH SQUARE 2023:rs.3.rs-2511186. [PMID: 36909567 PMCID: PMC10002837 DOI: 10.21203/rs.3.rs-2511186/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Within the field of amyloid and prion disease there is a need for a more comprehensive understanding of the fundamentals of disease biology. In order to facilitate the progression treatment and underpin comprehension of toxicity, fundamental understanding of the disruption to normal cellular biochemistry and trafficking is needed. Here, by removing the complex biochemistry of the brain, we have utilised known prion forming strains of Saccharomyces cerevisiae carrying different conformational variants of the Rnq1p to obtain Liquid Chromatography-Mass Spectrometry (LC-MS) metabolic profiles and identify key perturbations of prion presence. These studies reveal that prion containing [RNQ+] cells display a significant reduction in amino acid biosynthesis and distinct perturbations in sphingolipid metabolism, with significant downregulation in metabolites within these pathways. Moreover, that native Rnq1p appears to downregulate ubiquinone biosynthesis pathways within cells, suggesting that Rnq1p may play a lipid/mevalonate-based cytoprotective role as a regulator of ubiquinone production. These findings contribute to the understanding of how prion proteins interact in vivo in both their prion and non-prion confirmations and indicate potential targets for the mitigation of these effects. We demonstrate specific sphingolipid centred metabolic disruptions due to prion presence and give insight into a potential cytoprotective role of the native Rnq1 protein. This provides evidence of metabolic similarities between yeast and mammalian cells as a consequence of prion presence and establishes the application of metabolomics as a tool to investigate prion/amyloid-based phenomena.
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Du X, Dastmalchi F, Ye H, Garrett TJ, Diller MA, Liu M, Hogan WR, Brochhausen M, Lemas DJ. Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software. Metabolomics 2023; 19:11. [PMID: 36745241 DOI: 10.1007/s11306-023-01974-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a popular approach for metabolomics data acquisition and requires many data processing software tools. The FAIR Principles - Findability, Accessibility, Interoperability, and Reusability - were proposed to promote open science and reusable data management, and to maximize the benefit obtained from contemporary and formal scholarly digital publishing. More recently, the FAIR principles were extended to include Research Software (FAIR4RS). AIM OF REVIEW This study facilitates open science in metabolomics by providing an implementation solution for adopting FAIR4RS in the LC-HRMS metabolomics data processing software. We believe our evaluation guidelines and results can help improve the FAIRness of research software. KEY SCIENTIFIC CONCEPTS OF REVIEW We evaluated 124 LC-HRMS metabolomics data processing software obtained from a systematic review and selected 61 software for detailed evaluation using FAIR4RS-related criteria, which were extracted from the literature along with internal discussions. We assigned each criterion one or more FAIR4RS categories through discussion. The minimum, median, and maximum percentages of criteria fulfillment of software were 21.6%, 47.7%, and 71.8%. Statistical analysis revealed no significant improvement in FAIRness over time. We identified four criteria covering multiple FAIR4RS categories but had a low %fulfillment: (1) No software had semantic annotation of key information; (2) only 6.3% of evaluated software were registered to Zenodo and received DOIs; (3) only 14.5% of selected software had official software containerization or virtual machine; (4) only 16.7% of evaluated software had a fully documented functions in code. According to the results, we discussed improvement strategies and future directions.
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Affiliation(s)
- Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Farhad Dastmalchi
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Hao Ye
- Health Science Center Libraries, University of Florida, Florida, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Florida, USA
| | - Matthew A Diller
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mei Liu
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - William R Hogan
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mathias Brochhausen
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Dominick J Lemas
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA.
- Department of Obstetrics and Gynecology, University of Florida College of Medicine, Florida, Gainesville, United States.
- Center for Perinatal Outcomes Research, University of Florida College of Medicine, Gainesville, United States.
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Morabito A, De Simone G, Ferrario M, Falcetta F, Pastorelli R, Brunelli L. EASY-FIA: A Readably Usable Standalone Tool for High-Resolution Mass Spectrometry Metabolomics Data Pre-Processing. Metabolites 2022; 13:metabo13010013. [PMID: 36676938 PMCID: PMC9861133 DOI: 10.3390/metabo13010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Flow injection analysis coupled with high-resolution mass spectrometry (FIA-HRMS) is a fair trade-off between resolution and speed. However, free software available for data pre-processing is few, web-based, and often requires advanced user specialization. These tools rarely embedded blank and noise evaluation strategies, and direct feature annotation. We developed EASY-FIA, a free standalone application that can be employed for FIA-HRMS metabolomic data pre-processing by users with no bioinformatics/programming skills. We validated the tool's performance and applicability in two clinical metabolomics case studies. The main functions of our application are blank subtraction, alignment of the metabolites, and direct feature annotation by means of the Human Metabolome Database (HMDB) using a minimum number of mass spectrometry parameters. In a scenario where FIA-HRMS is increasingly recognized as a reliable strategy for fast metabolomics analysis, EASY-FIA could become a standardized and feasible tool easily usable by all scientists dealing with MS-based metabolomics. EASY-FIA was implemented in MATLAB with the App Designer tool and it is freely available for download.
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Affiliation(s)
- Aurelia Morabito
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Giulia De Simone
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Department of Biotechnologies and Biosciences, Università degli Studi Milano Bicocca, 20126 Milan, Italy
| | - Manuela Ferrario
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Francesca Falcetta
- Unit of Biophysics, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Roberta Pastorelli
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Laura Brunelli
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Correspondence: ; Tel.: +39-0239014742
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Peña-Bautista C, Álvarez-Sánchez L, Roca M, García-Vallés L, Baquero M, Cháfer-Pericás C. Plasma Lipidomics Approach in Early and Specific Alzheimer’s Disease Diagnosis. J Clin Med 2022; 11:jcm11175030. [PMID: 36078960 PMCID: PMC9457360 DOI: 10.3390/jcm11175030] [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: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background: The brain is rich in lipid content, so a physiopathological pathway in Alzheimer’s disease (AD) could be related to lipid metabolism impairment. The study of lipid profiles in plasma samples could help in the identification of early AD changes and new potential biomarkers. Methods: An untargeted lipidomic analysis was carried out in plasma samples from preclinical AD (n = 11), mild cognitive impairment-AD (MCI-AD) (n = 31), and healthy (n = 20) participants. Variables were identified by means of two complementary methods, and lipid families’ profiles were studied. Then, a targeted analysis was carried out for some identified lipids. Results: Statistically significant differences were obtained for the diglycerol (DG), lysophosphatidylethanolamine (LPE), lysophosphatidylcholine (LPC), monoglyceride (MG), and sphingomyelin (SM) families as well as for monounsaturated (MUFAs) lipids, among the participant groups. In addition, statistically significant differences in the levels of lipid families (ceramides (Cer), LPE, LPC, MG, and SM) were observed between the preclinical AD and healthy groups, while statistically significant differences in the levels of DG, MG, and PE were observed between the MCI-AD and healthy groups. In addition, 18:1 LPE showed statistically significant differences in the targeted analysis between early AD (preclinical and MCI) and healthy participants. Conclusion: The different plasma lipid profiles could be useful in the early and minimally invasive detection of AD. Among the lipid families, relevant results were obtained from DGs, LPEs, LPCs, MGs, and SMs. Specifically, MGs could be potentially useful in AD detection; while LPEs, LPCs, and SM seem to be more related to the preclinical stage, while DGs are more related to the MCI stage. Specifically, 18:1 LPE showed a potential utility as an AD biomarker.
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Affiliation(s)
- Carmen Peña-Bautista
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Lourdes Álvarez-Sánchez
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Marta Roca
- Analytical Unit, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Lorena García-Vallés
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Miguel Baquero
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Correspondence:
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12
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The Chemistry of Green and Roasted Coffee by Selectable 1D/2D Gas Chromatography Mass Spectrometry with Spectral Deconvolution. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165328. [PMID: 36014566 PMCID: PMC9414832 DOI: 10.3390/molecules27165328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
Abstract
Gas chromatography/mass spectrometry (GC/MS) is a long-standing technique for the analysis of volatile organic compounds (VOCs). When coupled with the Ion Analytics software, GC/MS provides unmatched selectivity in the analysis of complex mixtures and it reduces the reliance on high-resolution chromatography to obtain clean mass spectra. Here, we present an application of spectral deconvolution, with mass spectral subtraction, to identify a wide array of VOCs in green and roasted coffees. Automated sequential, two-dimensional GC-GC/MS of a roasted coffee sample produced the retention index and spectrum of 750 compounds. These initial analytes served as targets for subsequent coffee analysis by GC/MS. The workflow resulted in the quantitation of 511 compounds detected in two different green and roasted coffees. Of these, over 100 compounds serve as candidate differentiators of coffee quality, AAA vs. AA, as designated by the Coopedota cooperative in Costa Rica. Of these, 72 compounds survive the roasting process and can be used to discriminate green coffee quality after roasting.
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13
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MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools. Metabolites 2021; 11:metabo11100678. [PMID: 34677393 PMCID: PMC8540572 DOI: 10.3390/metabo11100678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 01/06/2023] Open
Abstract
The bottleneck for taking full advantage of metabolomics data is often the availability, awareness, and usability of analysis tools. Software tools specifically designed for metabolomics data are being developed at an increasing rate, with hundreds of available tools already in the literature. Many of these tools are open-source and freely available but are very diverse with respect to language, data formats, and stages in the metabolomics pipeline. To help mitigate the challenges of meeting the increasing demand for guidance in choosing analytical tools and coordinating the adoption of best practices for reproducibility, we have designed and built the MSCAT (Metabolomics Software CATalog) database of metabolomics software tools that can be sustainably and continuously updated. This database provides a survey of the landscape of available tools and can assist researchers in their selection of data analysis workflows for metabolomics studies according to their specific needs. We used machine learning (ML) methodology for the purpose of semi-automating the identification of metabolomics software tool names within abstracts. MSCAT searches the literature to find new software tools by implementing a Named Entity Recognition (NER) model based on a neural network model at the sentence level composed of a character-level convolutional neural network (CNN) combined with a bidirectional long-short-term memory (LSTM) layer and a conditional random fields (CRF) layer. The list of potential new tools (and their associated publication) is then forwarded to the database maintainer for the curation of the database entry corresponding to the tool. The end-user interface allows for filtering of tools by multiple characteristics as well as plotting of the aggregate tool data to monitor the metabolomics software landscape.
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14
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Gupta N, Ramakrishnan S, Wajid S. Emerging role of metabolomics in protein conformational disorders. Expert Rev Proteomics 2021; 18:395-410. [PMID: 34227444 DOI: 10.1080/14789450.2021.1948330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: Metabolomics focuses on interactions among different metabolites associated with various cellular functions in cells, tissues, and organs. In recent years, metabolomics has emerged as a powerful tool to identify perturbed metabolites, pathways influenced by the environment, for protein conformational diseases (PCDs) and also offers wide clinical application.Area Covered: This review provides a brief overview of recent advances in metabolomics as applied to identify metabolic variations in PCDs, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, prion disease, and cardiac amyloidosis. The 'PubMed' and 'Google Scholar' database search methods have been used to screen the published reports with key search terms: metabolomics, biomarkers, and protein conformational disorders.Expert opinion: Metabolomics is the large-scale study of metabolites and is deemed to overwhelm other omics. It plays a crucial role in finding variations in diseases due to protein conformational changes. However, many PCDs are yet to be identified. Metabolomics is still an emerging field; there is a need for new high-resolution analytical techniques and more studies need to be carried out to generate new information.
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Affiliation(s)
- Nimisha Gupta
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
| | | | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
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15
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Gadara D, Coufalikova K, Bosak J, Smajs D, Spacil Z. Systematic Feature Filtering in Exploratory Metabolomics: Application toward Biomarker Discovery. Anal Chem 2021; 93:9103-9110. [PMID: 34156818 DOI: 10.1021/acs.analchem.1c00816] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exploratory mass spectrometry-based metabolomics generates a plethora of features in a single analysis. However, >85% of detected features are typically false positives due to inefficient elimination of chimeric signals and chemical noise not relevant for biological and clinical data interpretation. The data processing is considered a bottleneck to unravel the translational potential in metabolomics. Here, we describe a systematic workflow to refine exploratory metabolomics data and reduce reported false positives. We applied the feature filtering workflow in a case/control study exploring common variable immunodeficiency (CVID). In the first stage, features were detected from raw liquid chromatography-mass spectrometry data by XCMS Online processing, blank subtraction, and reproducibility assessment. Detected features were annotated in metabolomics databases to produce a list of tentative identifications. We scrutinized tentative identifications' physicochemical properties, comparing predicted and experimental reversed-phase liquid chromatography (LC) retention time. A prediction model used a linear regression of 42 retention indices with the cLogP ranging from -6 to 11. The LC retention time probes the physicochemical properties and effectively reduces the number of tentatively identified metabolites, which are further submitted to statistical analysis. We applied the retention time-based analytical feature filtering workflow to datasets from the Metabolomics Workbench (www.metabolomicsworkbench.org), demonstrating the broad applicability. A subset of tentatively identified metabolites significantly different in CVID patients was validated by MS/MS acquisition to confirm potential CVID biomarkers' structures and virtually eliminate false positives. Our exploratory metabolomics data processing workflow effectively removes false positives caused by the chemical background and chimeric signals inherent to the analytical technique. It reduced the number of tentatively identified metabolites by 88%, from initially detected 6940 features in XCMS to 839 tentative identifications and streamlined consequent statistical analysis and data interpretation.
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Affiliation(s)
- Darshak Gadara
- RECETOX Centre, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Katerina Coufalikova
- RECETOX Centre, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Juraj Bosak
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic
| | - David Smajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic
| | - Zdenek Spacil
- RECETOX Centre, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
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16
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Misra BB. Advances in high resolution GC-MS technology: a focus on the application of GC-Orbitrap-MS in metabolomics and exposomics for FAIR practices. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2265-2282. [PMID: 33987631 DOI: 10.1039/d1ay00173f] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gas chromatography-mass spectrometry (GC-MS) provides a complementary analytical platform for capturing volatiles, non-polar and (derivatized) polar metabolites and exposures from a diverse array of matrixes. High resolution (HR) GC-MS as a data generation platform can capture data on analytes that are usually not detectable/quantifiable in liquid chromatography mass-spectrometry-based solutions. With the rise of high-resolution accurate mass (HRAM) GC-MS systems such as GC-Orbitrap-MS in the last decade after the time-of-flight (ToF) renaissance, numerous applications have been found in the fields of metabolomics and exposomics. In a short span of time, a multitude of studies have used GC-Orbitrap-MS to generate exciting new high throughput data spanning from diverse basic to applied research areas. The GC-Orbitrap-MS has found application in both targeted and untargeted efforts for capturing metabolomes and exposomes across diverse studies. In this review, I capture and summarize all the reported studies to date, and provide a snapshot of the milieu of commercial and open-source software solutions, spectral libraries, and informatics solutions available to a GC-Orbitrap-MS system instrument user or a data analyst dealing with these datasets. Lastly, but importantly, I provide an account on data sharing and meta-data capturing solutions that are available to make HRAM GC-MS based metabolomics and exposomics studies findable, accessible, interoperable, and reproducible (FAIR). These FAIR practices would allow data generators and users of GC-HRMS instruments to help the community of GC-MS researchers to collaborate and co-develop exciting tools and algorithms in the future.
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Affiliation(s)
- Biswapriya B Misra
- Independent Researcher, Pine-211, Raintree Park Dwaraka Krishna, Namburu, AP-522508, India.
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17
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Metabolomic-based clinical studies and murine models for acute pancreatitis disease: A review. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166123. [PMID: 33713791 DOI: 10.1016/j.bbadis.2021.166123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/21/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
Acute pancreatitis (AP) is one of the most common gastroenterological disorders requiring hospitalization and is associated with substantial morbidity and mortality. Metabolomics nowadays not only help us to understand cellular metabolism to a degree that was not previously obtainable, but also to reveal the importance of the metabolites in physiological control, disease onset and development. An in-depth understanding of metabolic phenotyping would be therefore crucial for accurate diagnosis, prognosis and precise treatment of AP. In this review, we summarized and addressed the metabolomics design and workflow in AP studies, as well as the results and analysis of the in-depth of research. Based on the metabolic profiling work in both clinical populations and experimental AP models, we described the metabolites with potential utility as biomarkers and the correlation between the altered metabolites and AP status. Moreover, the disturbed metabolic pathways correlated with biological function were discussed in the end. A practical understanding of current and emerging metabolomic approaches applicable to AP and use of the metabolite information presented will aid in designing robust metabolomics and biological experiments that result in identification of unique biomarkers and mechanisms, and ultimately enhanced clinical decision-making.
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18
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Rampler E, Abiead YE, Schoeny H, Rusz M, Hildebrand F, Fitz V, Koellensperger G. Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput. Anal Chem 2021; 93:519-545. [PMID: 33249827 PMCID: PMC7807424 DOI: 10.1021/acs.analchem.0c04698] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Evelyn Rampler
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Mate Rusz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Institute of Inorganic
Chemistry, University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Veronika Fitz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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19
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Dudek CA, Reuse C, Fuchs R, Hendriks J, Starck V, Hiller K. MIAMI--a tool for non-targeted detection of metabolic flux changes for mode of action identification. Bioinformatics 2020; 36:3925-3926. [PMID: 32324861 PMCID: PMC7320603 DOI: 10.1093/bioinformatics/btaa251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/13/2020] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Summary Mass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution-based (MID) similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled compounds between different conditions, targets of metabolic changes can be detected. Availability and implementation We implemented the data processing in C++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3.
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Affiliation(s)
- Christian-Alexander Dudek
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Regine Fuchs
- BASF Metabolome Solutions GmbH, Berlin 10589, Germany
| | | | - Veronique Starck
- BASF Metabolome Solutions GmbH, Berlin 10589, Germany.,BASF SE, Lampertheim 68623, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig 38106, Germany.,Department of Immunometabolism, Helmholtz Center for Infection Research, Braunschweig 38124, Germany
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20
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Dąbrowski Ł. Evaluation of a Simplified Method for GC/MS Qualitative Analysis of Polycyclic Aromatic Hydrocarbons, Polychlorinated Biphenyls, and Organic Pesticides Using PARADISe Computer Program. Molecules 2020; 25:molecules25163727. [PMID: 32824143 PMCID: PMC7465948 DOI: 10.3390/molecules25163727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 11/16/2022] Open
Abstract
For complex matrices such as environmental samples, there is usually a problem with not fully resolved peaks during GC/MS analysis. The PARADISe computer program (based on the PARFAC2 model) allows the identification of peaks using the deconvoluted mass spectra and the NIST MS library. The number of repetitions required by this software (at least five) is a real limitation for the determination of semi-volatile compounds, like polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and organic pesticides in environmental samples. In this work, the method to overcome this condition was proposed and evaluated. The sets of the five files required by PARADISe were prepared by mathematically modifying the original GC/MS chromatograms obtained for the standard mixture (C = 2 µg/mL of 40 compounds) and real sample extracts (soil samples with different total organic carbon content and one cardboard extract) spiked with standards. Total average match factor for all the substances identified in a standard mixture was 874 (near 900—“excellent match”), and for all the substances in the real samples, it was 786 (near 800—“good match”). The results from PARADISe were comparable to those obtained with other programs: AMDIS (NIST) and MassHunter (Agilent), tested also in this work. PARADISe software can be effectively used for chromatogram deconvolution and substance identification.
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Affiliation(s)
- Łukasz Dąbrowski
- Department of Food Analysis and Environmental Protection, Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, 3 Seminaryjna Street, 85-326 Bydgoszcz, Poland
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21
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McGee EE, Kiblawi R, Playdon MC, Eliassen AH. Nutritional Metabolomics in Cancer Epidemiology: Current Trends, Challenges, and Future Directions. Curr Nutr Rep 2020; 8:187-201. [PMID: 31129888 DOI: 10.1007/s13668-019-00279-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Metabolomics offers several opportunities for advancement in nutritional cancer epidemiology; however, numerous research gaps and challenges remain. This narrative review summarizes current research, challenges, and future directions for epidemiologic studies of nutritional metabolomics and cancer. RECENT FINDINGS Although many studies have used metabolomics to investigate either dietary exposures or cancer, few studies have explicitly investigated diet-cancer relationships using metabolomics. Most studies have been relatively small (≤ ~ 250 cases) or have assessed a limited number of nutritional metabolites (e.g., coffee or alcohol-related metabolites). Nutritional metabolomic investigations of cancer face several challenges in study design; biospecimen selection, handling, and processing; diet and metabolite measurement; statistical analyses; and data sharing and synthesis. More metabolomics studies linking dietary exposures to cancer risk, prognosis, and survival are needed, as are biomarker validation studies, longitudinal analyses, and methodological studies. Despite the remaining challenges, metabolomics offers a promising avenue for future dietary cancer research.
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Affiliation(s)
- Emma E McGee
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Rama Kiblawi
- Division of Cancer Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Mary C Playdon
- Division of Cancer Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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22
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Lefort G, Liaubet L, Canlet C, Tardivel P, Père MC, Quesnel H, Paris A, Iannuccelli N, Vialaneix N, Servien R. ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra. Bioinformatics 2020; 35:4356-4363. [PMID: 30977816 DOI: 10.1093/bioinformatics/btz248] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/01/2019] [Accepted: 04/08/2019] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION In metabolomics, the detection of new biomarkers from Nuclear Magnetic Resonance (NMR) spectra is a promising approach. However, this analysis remains difficult due to the lack of a whole workflow that handles spectra pre-processing, automatic identification and quantification of metabolites and statistical analyses, in a reproducible way. RESULTS We present ASICS, an R package that contains a complete workflow to analyse spectra from NMR experiments. It contains an automatic approach to identify and quantify metabolites in a complex mixture spectrum and uses the results of the quantification in untargeted and targeted statistical analyses. ASICS was shown to improve the precision of quantification in comparison to existing methods on two independent datasets. In addition, ASICS successfully recovered most metabolites that were found important to explain a two level condition describing the samples by a manual and expert analysis based on bucketing. It also found new relevant metabolites involved in metabolic pathways related to risk factors associated with the condition. AVAILABILITY AND IMPLEMENTATION ASICS is distributed as an R package, available on Bioconductor. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gaëlle Lefort
- MIAT, Université de Toulouse, INRA, Castanet Tolosan, France.,GenPhySE, Université de Toulouse, INRA, ENVT, Castanet Tolosan, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRA, ENVT, Castanet Tolosan, France
| | - Cécile Canlet
- Toxalim, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France.,Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Patrick Tardivel
- Institute of Mathematics, University of Wroclaw, Wroclaw 50-384, Poland
| | | | | | - Alain Paris
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle, CNRS, CP54, Paris, France
| | | | | | - Rémi Servien
- INTHERES, Université de Toulouse, INRA, ENVT, Toulouse, France
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23
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Rashad S, Saigusa D, Yamazaki T, Matsumoto Y, Tomioka Y, Saito R, Uruno A, Niizuma K, Yamamoto M, Tominaga T. Metabolic basis of neuronal vulnerability to ischemia; an in vivo untargeted metabolomics approach. Sci Rep 2020; 10:6507. [PMID: 32300196 PMCID: PMC7162929 DOI: 10.1038/s41598-020-63483-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 03/27/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the root causes of neuronal vulnerability to ischemia is paramount to the development of new therapies for stroke. Transient global cerebral ischemia (tGCI) leads to selective neuronal cell death in the CA1 sub-region of the hippocampus, while the neighboring CA3 sub-region is left largely intact. By studying factors pertaining to such selective vulnerability, we can develop therapies to enhance outcome after stroke. Using untargeted liquid chromatography-mass spectrometry, we analyzed temporal metabolomic changes in CA1 and CA3 hippocampal areas following tGCI in rats till the setting of neuronal apoptosis. 64 compounds in CA1 and 74 in CA3 were found to be enriched and statistically significant following tGCI. Pathway analysis showed that pyrimidine and purine metabolism pathways amongst several others to be enriched after tGCI in CA1 and CA3. Metabolomics analysis was able to capture very early changes following ischemia. We detected 6 metabolites to be upregulated and 6 to be downregulated 1 hour after tGCI in CA1 versus CA3. Several metabolites related to apoptosis and inflammation were differentially expressed in both regions after tGCI. We offer a new insight into the process of neuronal apoptosis, guided by metabolomic profiling that was not performed to such an extent previously.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan. .,Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Takahiro Yamazaki
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yotaro Matsumoto
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Ritsumi Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan. .,Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan. .,Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan.
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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24
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Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics. Methods Mol Biol 2020; 2064:191-217. [PMID: 31565776 DOI: 10.1007/978-1-4939-9831-9_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this age of -omics data-guided big data revolution, metabolomics has received significant attention as compared to genomics, transcriptomics, and proteomics for its proximity to the phenotype, the promises it makes and the challenges it throws. Although metabolomes of entire organisms, organs, biofluids, and tissues are of immense interest, a cell-specific resolution is deemed critical for biomedical applications where a granular understanding of cellular metabolism at cell-type and subcellular resolution is desirable. Mass spectrometry (MS) is a versatile technique that is used to analyze a broad range of compounds from different species and cell-types, with high accuracy, resolution, sensitivity, selectivity, and fast data acquisition speeds. With recent advances in MS and spectroscopy-based platforms, the research community is able to generate high-throughput data sets from single cells. However, it is challenging to handle, store, process, analyze, and interpret data in a routine manner. In this treatise, I present a workflow of metabolomics data generation from single cells and single-cell types to their analysis, visualization, and interpretation for obtaining biological insights.
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25
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Peña-Bautista C, Roca M, López-Cuevas R, Baquero M, Vento M, Cháfer-Pericás C. Metabolomics study to identify plasma biomarkers in alzheimer disease: ApoE genotype effect. J Pharm Biomed Anal 2019; 180:113088. [PMID: 31923717 DOI: 10.1016/j.jpba.2019.113088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/03/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022]
Abstract
Alzheimer Disease (AD) is the main cause of dementia, and it has a great social and economic impact worldwide. It is a complex multifactorial disease, and we still do not know enough about its causes. For this reason, omics studies could be a useful tool for the search for new biomarkers and for enhancing the knowledge of different metabolic pathways that may be altered in the initial stages of the disease. Metabolomic analysis was carried out for plasma samples from early AD patients and healthy controls. Obtained data were normalized and analyzed by volcano plot and supervised orthogonal-least-squares-discriminant analysis. Fifteen variables were selected as the most important variables for the groups' discrimination, and the different levels of 6 identified metabolites could discriminate between patients with different ApoE4 genotypes (ε4-carriers and non ε4-carriers). In conclusion, ApoE4 genotype is associated with changes in lipid metabolomics profile in AD patients, and it could be relevant for the development of AD since early stages.
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Affiliation(s)
| | - Marta Roca
- Analytical Unit Platform, Health Research Institute La Fe, Valencia, Spain
| | | | - Miguel Baquero
- Neurology Unit, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Máximo Vento
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Spain
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Germeys C, Vandoorne T, Bercier V, Van Den Bosch L. Existing and Emerging Metabolomic Tools for ALS Research. Genes (Basel) 2019; 10:E1011. [PMID: 31817338 PMCID: PMC6947647 DOI: 10.3390/genes10121011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/23/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Growing evidence suggests that aberrant energy metabolism could play an important role in the pathogenesis of amyotrophic lateral sclerosis (ALS). Despite this, studies applying advanced technologies to investigate energy metabolism in ALS remain scarce. The rapidly growing field of metabolomics offers exciting new possibilities for ALS research. Here, we review existing and emerging metabolomic tools that could be used to further investigate the role of metabolism in ALS. A better understanding of the metabolic state of motor neurons and their surrounding cells could hopefully result in novel therapeutic strategies.
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Affiliation(s)
- Christine Germeys
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Tijs Vandoorne
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Valérie Bercier
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, 3000 Leuven, Belgium; (C.G.); (T.V.); (V.B.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
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27
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Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites 2019; 9:E200. [PMID: 31548506 PMCID: PMC6835268 DOI: 10.3390/metabo9100200] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 11/17/2022] Open
Abstract
Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.
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Affiliation(s)
- Jan Stanstrup
- Preventive and Clinical Nutrition, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark.
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany.
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Thomas Naake
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
| | - Luca Nicolotti
- The Australian Wine Research Institute, Metabolomics Australia, PO Box 197, Adelaide SA 5064, Australia.
| | - Kristian Peters
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.
| | - Reza M Salek
- The International Agency for Research on Cancer, 150 cours Albert Thomas, CEDEX 08, 69372 Lyon, France.
| | - Tobias Schulze
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg.
| | - Michael A Stravs
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dubendorf, Switzerland.
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Sciences and Decision, MetaboHUB, Gif-Sur-Yvette F-91191, France.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Ralf J M Weber
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
- Chair of Analytical Food Chemistry, Technische Universität München, 85354 Weihenstephan, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig Deutscher, Platz 5e, 04103 Leipzig, Germany.
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28
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Kumar A, Misra BB. Challenges and Opportunities in Cancer Metabolomics. Proteomics 2019; 19:e1900042. [PMID: 30950571 DOI: 10.1002/pmic.201900042] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/22/2019] [Indexed: 12/23/2022]
Abstract
Challenges in metabolomics for a given spectrum of disease are more or less comparable, ranging from the accurate measurement of metabolite abundance, compound annotation, identification of unknown constituents, and interpretation of untargeted and analysis of high throughput targeted metabolomics data leading to the identification of biomarkers. However, metabolomics approaches in cancer studies specifically suffer from several additional challenges and require robust ways to sample the cells and tissues in order to tackle the constantly evolving cancer landscape. These constraints include, but are not limited to, discriminating the signals from given cell types and those that are cancer specific, discerning signals that are systemic and confounded, cell culture-based challenges associated with cell line identities and media standardizations, the need to look beyond Warburg effects, citrate cycle, lactate metabolism, and identifying and developing technologies to precisely and effectively sample and profile the heterogeneous tumor environment. This review article discusses some of the current and pertinent hurdles in cancer metabolomics studies. In addition, it addresses some of the most recent and exciting developments in metabolomics that may address some of these issues. The aim of this article is to update the oncometabolomics research community about the challenges and potential solutions to these issues.
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Affiliation(s)
- Ashish Kumar
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX, 78227, USA
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA
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29
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Misra B. Individualized metabolomics: opportunities and challenges. Clin Chem Lab Med 2019; 58:939-947. [DOI: 10.1515/cclm-2019-0130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 03/04/2019] [Indexed: 12/23/2022]
Abstract
Abstract
The goal of advancing science in health care is to provide high quality treatment and therapeutic opportunities to patients in need. This is especially true in precision medicine, wherein the ultimate goal is to link disease phenotypes to targeted treatments and novel therapeutics at the scale of an individual. With the advent of -omics technologies, such as genomics, proteomics, microbiome, among others, the metabolome is of wider and immediate interest for its important role in metabolic regulation. The metabolome, of course, comes with its own questions regarding technological challenges. In this opinion article, I attempt to interrogate some of the main challenges associated with individualized metabolomics, and available opportunities in the context of its clinical application. Some questions this article addresses and attempts to find answers for are: Can a personal metabolome (n = 1) be inexpensive, affordable and informative enough (i.e. provide predictive yet validated biomarkers) to represent the entirety of a population? How can a personal metabolome complement advances in other -omics areas and the use of monitoring devices, which occupy our personal space?
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Affiliation(s)
- Biswapriya Misra
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine , Wake Forest University School of Medicine , Medical Center Boulevard , Winston-Salem, 27157 NC , USA
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30
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Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem 2019; 91:3302-3310. [PMID: 30688441 PMCID: PMC6660005 DOI: 10.1021/acs.analchem.8b04310] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/28/2019] [Indexed: 12/29/2022]
Abstract
Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition, and reanalysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society, we have created mzTab-M to act as a common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g., LC-MS, GC-MS, DIMS, etc.) and different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.
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Affiliation(s)
- Nils Hoffmann
- Leibniz-Institut
für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - Joel Rein
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Timo Sachsenberg
- Applied Bioinformatics
Group, Center for Bioinformatics, University
of Tübingen, Sand
14, 72076 Tübingen, Germany
| | - Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
- Center
for Explorative Lipidomics, BioTechMed-Graz, 8010 Graz, Austria
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Gerhard Mayer
- Medizinisches Proteom Center (MPC), Ruhr-Universität
Bochum, Universitätsstraße
150, D-44801 Bochum, Germany
| | - Oliver Alka
- Applied Bioinformatics
Group, Center for Bioinformatics, University
of Tübingen, Sand
14, 72076 Tübingen, Germany
| | - Saravanan Dayalan
- Metabolomics Australia, The University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Jake T. M. Pearce
- MRC-NIHR National Phenome Centre, Department of Surgery & Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Philippe Rocca-Serra
- University of Oxford, e-Research Centre, 7 Keble Road, Oxford OX1
3QG, United Kingdom
| | - Da Qi
- BGI-Shenzhen, Shenzhen, 518083, People’s Republic of China
- Institute
of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Martin Eisenacher
- Medizinisches Proteom Center (MPC), Ruhr-Universität
Bochum, Universitätsstraße
150, D-44801 Bochum, Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Reza M. Salek
- International Agency for Research on Cancer, 150 cours Albert Thomas, 69008 Lyon, France
| | - Steffen Neumann
- Department
of Stress and Developmental Biology, Leibniz
Institute of Plant Biochemistry, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig Deutscher, Platz
5e, 04103 Leipzig, Germany
| | - Andrew R. Jones
- Institute
of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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31
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Eisenreich W, Rudel T, Heesemann J, Goebel W. How Viral and Intracellular Bacterial Pathogens Reprogram the Metabolism of Host Cells to Allow Their Intracellular Replication. Front Cell Infect Microbiol 2019; 9:42. [PMID: 30886834 PMCID: PMC6409310 DOI: 10.3389/fcimb.2019.00042] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Viruses and intracellular bacterial pathogens (IBPs) have in common the need of suitable host cells for efficient replication and proliferation during infection. In human infections, the cell types which both groups of pathogens are using as hosts are indeed quite similar and include phagocytic immune cells, especially monocytes/macrophages (MOs/MPs) and dendritic cells (DCs), as well as nonprofessional phagocytes, like epithelial cells, fibroblasts and endothelial cells. These terminally differentiated cells are normally in a metabolically quiescent state when they are encountered by these pathogens during infection. This metabolic state of the host cells does not meet the extensive need for nutrients required for efficient intracellular replication of viruses and especially IBPs which, in contrast to the viral pathogens, have to perform their own specific intracellular metabolism to survive and efficiently replicate in their host cell niches. For this goal, viruses and IBPs have to reprogram the host cell metabolism in a pathogen-specific manner to increase the supply of nutrients, energy, and metabolites which have to be provided to the pathogen to allow its replication. In viral infections, this appears to be often achieved by the interaction of specific viral factors with central metabolic regulators, including oncogenes and tumor suppressors, or by the introduction of virus-specific oncogenes. Less is so far known on the mechanisms leading to metabolic reprogramming of the host cell by IBPs. However, the still scant data suggest that similar mechanisms may also determine the reprogramming of the host cell metabolism in IBP infections. In this review, we summarize and compare the present knowledge on this important, yet still poorly understood aspect of pathogenesis of human viral and especially IBP infections.
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Affiliation(s)
- Wolfgang Eisenreich
- Chair of Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany
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32
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Domingo-Almenara X, Montenegro-Burke JR, Guijas C, Majumder ELW, Benton HP, Siuzdak G. Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics. Anal Chem 2019; 91:3246-3253. [PMID: 30681830 DOI: 10.1021/acs.analchem.8b03126] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Computational metabolite annotation in untargeted profiling aims at uncovering neutral molecular masses of underlying metabolites and assign those with putative identities. Existing annotation strategies rely on the observation and annotation of adducts to determine metabolite neutral masses. However, a significant fraction of features usually detected in untargeted experiments remains unannotated, which limits our ability to determine neutral molecular masses. Despite the availability of tools to annotate, relatively few of them benefit from the inherent presence of in-source fragments in liquid chromatography-electrospray ionization-mass spectrometry. In this study, we introduce a strategy to annotate in-source fragments in untargeted data using low-energy tandem mass spectrometry (MS) spectra from the METLIN library. Our algorithm, MISA (METLIN-guided in-source annotation), compares detected features against low-energy fragments from MS/MS spectra, enabling robust annotation and putative identification of metabolic features based on low-energy spectral matching. The algorithm was evaluated through an annotation analysis of a total of 140 metabolites across three different sets of biological samples analyzed with liquid chromatography-mass spectrometry. Results showed that, in cases where adducts were not formed or detected, MISA was able to uncover neutral molecular masses by in-source fragment matching. MISA was also able to provide putative metabolite identities via two annotation scores. These scores take into account the number of in-source fragments matched and the relative intensity similarity between the experimental data and the reference low-energy MS/MS spectra. Overall, results showed that in-source fragmentation is a highly frequent phenomena that should be considered for comprehensive feature annotation. Thus, combined with adduct annotation, this strategy adds a complementary annotation layer, enabling in-source fragments to be annotated and increasing putative identification confidence. The algorithm is integrated into the XCMS Online platform and is freely available at http://xcmsonline.scripps.edu .
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33
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Markley JL, Dashti H, Wedell JR, Westler WM, Eghbalnia HR. Tools for Enhanced NMR-Based Metabolomics Analysis. Methods Mol Biol 2019; 2037:413-427. [PMID: 31463858 PMCID: PMC7995344 DOI: 10.1007/978-1-4939-9690-2_23] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolomics is the study of profiles of small molecules in biological fluids, cells, or organs. These profiles can be thought of as the "fingerprints" left behind from chemical processes occurring in biological systems. Because of its potential for groundbreaking applications in disease diagnostics, biomarker discovery, and systems biology, metabolomics has emerged as a rapidly growing area of research. Metabolomics investigations often, but not always, involve the identification and quantification of endogenous and exogenous metabolites in biological samples. Software tools and databases play a crucial role in advancing the rigor, robustness, reproducibility, and validation of these studies. Specifically, the establishment of a robust library of spectral signatures with unique compound descriptors and atom identities plays a key role in profiling studies based on data from nuclear magnetic resonance (NMR) spectroscopy. Here, we discuss developments leading to a rigorous basis for unique identification of compounds, reproducible numbering of atoms, the compact representation of NMR spectra of metabolites and small molecules, tools for improved compound identification, quantification and visualization, and approaches toward the goal of rigorous analysis of metabolomics data.
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Affiliation(s)
- John L Markley
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA.
| | - Hesam Dashti
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan R Wedell
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
| | - William M Westler
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
| | - Hamid R Eghbalnia
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
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Gupta L, Ahmed S, Jain A, Misra R. Emerging role of metabolomics in rheumatology. Int J Rheum Dis 2018; 21:1468-1477. [PMID: 30146741 DOI: 10.1111/1756-185x.13353] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/21/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022]
Abstract
The pursuit for understanding disease pathogenesis, in this age of rapid laboratory diagnostics and fast-paced research, has led scientists worldwide to take recourse in hypothesis-free approaches for molecular diagnosis. Metabolomics is one such powerful tool that explores comprehensibly the metabolic alternations in human diseases. It involves study of small molecules of less than 1 kD in size by either LSMS or nuclear magnetic resonance. Unlike genomics, which tells us what may have happened, metabolomics reflects what did happen. The NMR technique has an advantage of analyzing metabolites without sample preparation, thereby diminishing artifacts, is less cumbersome and with the latest database on Metabolome; about 30 000 metabolites can be identified. The study of metabolomics for several rheumatic diseases, including rheumatoid arthritis, lupus, osteoarthritis and vasculitis, has revealed distinctive metabolic signatures. Thus, metabolomics is a technique that promises precision medicine with better biomarkers, robust predictors of drug response and of disease outcome, discovery of newer metabolites and pathways in disease pathogenesis, and finally, targeted drug development. This review intends to decipher its relevance in common rheumatic diseases.
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Affiliation(s)
- Latika Gupta
- Department of Clinical Immunology and Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sakir Ahmed
- Department of Clinical Immunology and Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Avinash Jain
- Department of Clinical Immunology and Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ramnath Misra
- Department of Clinical Immunology and Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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35
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Misra BB, Mohapatra S. Tools and resources for metabolomics research community: A 2017-2018 update. Electrophoresis 2018; 40:227-246. [PMID: 30443919 DOI: 10.1002/elps.201800428] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023]
Abstract
The scale at which MS- and NMR-based platforms generate metabolomics datasets for both research, core, and clinical facilities to address challenges in the various sciences-ranging from biomedical to agricultural-is underappreciated. Thus, metabolomics efforts spanning microbe, environment, plant, animal, and human systems have led to continual and concomitant growth of in silico resources for analysis and interpretation of these datasets. These software tools, resources, and databases drive the field forward to help keep pace with the amount of data being generated and the sophisticated and diverse analytical platforms that are being used to generate these metabolomics datasets. To address challenges in data preprocessing, metabolite annotation, statistical interrogation, visualization, interpretation, and integration, the metabolomics and informatics research community comes up with hundreds of tools every year. The purpose of the present review is to provide a brief and useful summary of more than 95 metabolomics tools, software, and databases that were either developed or significantly improved during 2017-2018. We hope to see this review help readers, developers, and researchers to obtain informed access to these thorough lists of resources for further improvisation, implementation, and application in due course of time.
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Affiliation(s)
- Biswapriya B Misra
- Department of Internal Medicine, Section of Molecular Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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36
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Wolfender JL, Nuzillard JM, van der Hooft JJJ, Renault JH, Bertrand S. Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics. Anal Chem 2018; 91:704-742. [DOI: 10.1021/acs.analchem.8b05112] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | | | - Jean-Hugues Renault
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, 44035 Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, 44035 Nantes, France
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37
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Prasannan CB, Jaiswal D, Davis R, Wangikar PP. An improved method for extraction of polar and charged metabolites from cyanobacteria. PLoS One 2018; 13:e0204273. [PMID: 30286115 PMCID: PMC6171824 DOI: 10.1371/journal.pone.0204273] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/05/2018] [Indexed: 12/30/2022] Open
Abstract
A key requirement for 13C Metabolic flux analysis (13C-MFA), a widely used technique to estimate intracellular metabolic fluxes, is an efficient method for the extraction of intermediate metabolites for analysis via liquid chromatography mass spectrometry (LC/MS). The 13C isotopic labeling results in further distribution of an already sparse pool of intermediate metabolites into isotopologues, each appearing as a separate chromatographic feature. We examined some of the reported solvent systems for the extraction of polar intracellular metabolites from three strains of cyanobacteria of the genus Synechococcus, viz., Synechococcus sp. PCC 7002, Synechococcus elongatus PCC 7942, and a newly isolated Synechococcus elongatus PCC 11801 (manuscript under review). High resolution-LC/MS was used to assess the relative abundance of the extracted metabolites. The different solvent systems used for extraction led to statistically significant changes in the extraction efficiency for a large number of metabolites. While a few hundred m/z features or potential metabolites were detected with different solvent systems, the abundance of over a quarter of all metabolites varied significantly from one solvent system to another. Further, the extraction methods were evaluated for a targeted set of metabolites that are important in 13C-MFA studies of photosynthetic organisms. While for the strain PCC 7002, the reported method using methanol-chloroform-water system gave satisfactory results, a mild base in the form of NH4OH had to be used in place of water to achieve adequate levels of extraction for PCC 7942 and PCC 11801. While minor changes in extraction solvent resulted in dramatic changes in the extraction efficiency of a number of compounds, certain metabolites such as amino acids and organic acids were adequately extracted in all the solvent systems tested. Overall, we present a new improved method for extraction using a methanol-chloroform-NH4OH system. Our method improves the extraction of polar compounds such as sugar phosphates, bisphosphates, that are central to 13C-MFA studies.
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Affiliation(s)
- Charulata B. Prasannan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rose Davis
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Pramod P. Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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38
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Blaženović I, Shen T, Mehta SS, Kind T, Ji J, Piparo M, Cacciola F, Mondello L, Fiehn O. Increasing Compound Identification Rates in Untargeted Lipidomics Research with Liquid Chromatography Drift Time-Ion Mobility Mass Spectrometry. Anal Chem 2018; 90:10758-10764. [PMID: 30096227 DOI: 10.1021/acs.analchem.8b01527] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Unknown metabolites represent a bottleneck in untargeted metabolomics research. Ion mobility-mass spectrometry (IM-MS) facilitates lipid identification because it yields collision cross section (CCS) information that is independent from mass or lipophilicity. To date, only a few CCS values are publicly available for complex lipids such as phosphatidylcholines, sphingomyelins, or triacylglycerides. This scarcity of data limits the use of CCS values as an identification parameter that is orthogonal to mass, MS/MS, or retention time. A combination of lipid descriptors was used to train five different machine learning algorithms for automatic lipid annotations, combining accurate mass ( m/ z), retention time (RT), CCS values, carbon number, and unsaturation level. Using a training data set of 429 true positive lipid annotations from four lipid classes, 92.7% correct annotations overall were achieved using internal cross-validation. The trained prediction model was applied to an unknown milk lipidomics data set and allowed for class 3 level annotations of most features detected in this application set according to Metabolomics Standards Initiative (MSI) reporting guidelines.
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Affiliation(s)
- Ivana Blaženović
- West Coast Metabolomics Center , UC Davis , Davis , California 95616 , United States
| | - Tong Shen
- West Coast Metabolomics Center , UC Davis , Davis , California 95616 , United States
| | - Sajjan S Mehta
- West Coast Metabolomics Center , UC Davis , Davis , California 95616 , United States
| | - Tobias Kind
- West Coast Metabolomics Center , UC Davis , Davis , California 95616 , United States
| | - Jian Ji
- West Coast Metabolomics Center , UC Davis , Davis , California 95616 , United States.,School of Food Science, State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, School of Food Science Synergetic Innovation Center of Food Safety and Nutrition , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Marco Piparo
- West Coast Metabolomics Center , UC Davis , Davis , California 95616 , United States.,Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali , University of Messina-Polo Annunziata , Viale Annunziata , 98168 Messina , Italy
| | - Francesco Cacciola
- Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali , University of Messina , Via Consolare Valeria , 98125 Messina , Italy
| | - Luigi Mondello
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali , University of Messina-Polo Annunziata , Viale Annunziata , 98168 Messina , Italy.,Chromaleont s.r.l., c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Polo Annunziata , University of Messina , viale Annunziata , 98168 Messina , Italy.,Department of Medicine , University Campus Bio-Medico of Rome , Via Álvaro del Portillo 21 , 00128 Rome , Italy
| | - Oliver Fiehn
- West Coast Metabolomics Center , UC Davis , Davis , California 95616 , United States.,Department of Biochemistry , King Abdulaziz University , Jeddah 21589 , Saudi Arabia
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39
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Chaleckis R, Meister I, Zhang P, Wheelock CE. Challenges, progress and promises of metabolite annotation for LC-MS-based metabolomics. Curr Opin Biotechnol 2018; 55:44-50. [PMID: 30138778 DOI: 10.1016/j.copbio.2018.07.010] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
Abstract
Accurate annotation is vital for data interpretation; however, metabolite identification is a major bottleneck in untargeted metabolomics. Although community guidelines for metabolite identification were published over a decade ago, adaptation of the recommended standards has been limited. The complexity of LC-MS data due to combinations of various chromatographic and mass spectrometric acquisition methods has resulted in the advent of diverse workflows, which often involve non-standardized manual curation. Herein, we review the parameters involved in metabolite reporting and provide a workflow to estimate the level of confidence in reported metabolite annotation. The future of metabolite identification will be heavily based upon the use of metabolome data repositories and associated data analysis tools, which will enable data to be shared, re-analyzed and re-annotated in an automated fashion.
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Affiliation(s)
- Romanas Chaleckis
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Isabel Meister
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pei Zhang
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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40
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Misra BB, Langefeld CD, Olivier M, Cox LA. Integrated Omics: Tools, Advances, and Future Approaches. J Mol Endocrinol 2018; 62:JME-18-0055. [PMID: 30006342 DOI: 10.1530/jme-18-0055] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
Abstract
With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized data files on a daily basis. These data file sizes, together with differences in nomenclature among these data types, make the integration of these multi-dimensional omics data into biologically meaningful context challenging. Variously named as integrated omics, multi-omics, poly-omics, trans-omics, pan-omics, or shortened to just 'omics', the challenges include differences in data cleaning, normalization, biomolecule identification, data dimensionality reduction, biological contextualization, statistical validation, data storage and handling, sharing, and data archiving. The ultimate goal is towards the holistic realization of a 'systems biology' understanding of the biological question in hand. Commonly used approaches in these efforts are currently limited by the 3 i's - integration, interpretation, and insights. Post integration, these very large datasets aim to yield unprecedented views of cellular systems at exquisite resolution for transformative insights into processes, events, and diseases through various computational and informatics frameworks. With the continued reduction in costs and processing time for sample analyses, and increasing types of omics datasets generated such as glycomics, lipidomics, microbiomics, and phenomics, an increasing number of scientists in this interdisciplinary domain of bioinformatics face these challenges. We discuss recent approaches, existing tools, and potential caveats in the integration of omics datasets for development of standardized analytical pipelines that could be adopted by the global omics research community.
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Affiliation(s)
- Biswapriya B Misra
- B Misra, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Carl D Langefeld
- C Langefeld, Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Michael Olivier
- M Olivier, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Laura A Cox
- L Cox, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
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41
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Blaženović I, Kind T, Ji J, Fiehn O. Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics. Metabolites 2018; 8:E31. [PMID: 29748461 PMCID: PMC6027441 DOI: 10.3390/metabo8020031] [Citation(s) in RCA: 402] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 04/26/2018] [Accepted: 05/06/2018] [Indexed: 01/17/2023] Open
Abstract
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.
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Affiliation(s)
- Ivana Blaženović
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
| | - Tobias Kind
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science of Jiangnan University, School of Food Science Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China.
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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42
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Current and future perspectives of functional metabolomics in disease studies-A review. Anal Chim Acta 2018; 1037:41-54. [PMID: 30292314 DOI: 10.1016/j.aca.2018.04.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/20/2018] [Accepted: 04/13/2018] [Indexed: 12/16/2022]
Abstract
Functional metabolomics is a new concept, which studies the functions of metabolites and related enzymes focused on metabolomics. It overcomes the shortcomings of traditional discovery metabolomics of mainly relying on literatures for biological interpretation. Functional metabolomics has many advantages. Firstly, the functional roles of metabolites and related metabolic enzymes are focused. Secondly, the in vivo and in vitro experiments are conducted to validate the metabolomics findings, therefore, increasing the reliability of metabolomics study and producing the new knowledge. Thirdly, functional metabolomics can be used by biologists to investigate functions of metabolites, and related genes and proteins. In this review, we summarize the analytical, biological and clinical platforms used in functional metabolomics studies. Recent progresses of functional metabolomics in cancer, metabolic diseases and biological phenotyping are reviewed, and future development is also predicted. Because of the tremendous advantages of functional metabolomics, it will have a bright future.
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