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Wu Y, Sanati O, Uchimiya M, Krishnamurthy K, Wedell J, Hoch JC, Edison AS, Delaglio F. SAND: Automated Time-Domain Modeling of NMR Spectra Applied to Metabolite Quantification. Anal Chem 2024; 96:1843-1851. [PMID: 38273718 PMCID: PMC10896553 DOI: 10.1021/acs.analchem.3c03078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
Developments in untargeted nuclear magnetic resonance (NMR) metabolomics enable the profiling of thousands of biological samples. The exploitation of this rich source of information requires a detailed quantification of spectral features. However, the development of a consistent and automatic workflow has been challenging because of extensive signal overlap. To address this challenge, we introduce the software Spectral Automated NMR Decomposition (SAND). SAND follows on from the previous success of time-domain modeling and automatically quantifies entire spectra without manual interaction. The SAND approach uses hybrid optimization with Markov chain Monte Carlo methods, employing subsampling in both time and frequency domains. In particular, SAND randomly divides the time-domain data into training and validation sets to help avoid overfitting. We demonstrate the accuracy of SAND, which provides a correlation of ∼0.9 with ground truth on cases including highly overlapped simulated data sets, a two-compound mixture, and a urine sample spiked with different amounts of a four-compound mixture. We further demonstrate an automated annotation using correlation networks derived from SAND decomposed peaks, and on average, 74% of peaks for each compound can be recovered in single clusters. SAND is available in NMRbox, the cloud computing environment for NMR software hosted by the Network for Advanced NMR (NAN). Since the SAND method uses time-domain subsampling (i.e., random subset of time-domain points), it has the potential to be extended to a higher dimensionality and nonuniformly sampled data.
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Affiliation(s)
- Yue Wu
- Institute
of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Omid Sanati
- School
of Electrical and Computer Engineering, University of Georgia, Athens, Georgia 30602, United States
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Mario Uchimiya
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | | | - Jonathan Wedell
- National
Magnetic Resonance Facility, University
of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey C. Hoch
- Department
of Molecular Biology and Biophysics, University
of Connecticut, Farmington, Connecticut 06030-3305, United States
| | - Arthur S. Edison
- Institute
of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Frank Delaglio
- Institute
for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University
of Maryland, Rockville, Maryland 20850, United States
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Alexandersson E, Sandström C, Meijer J, Nestor G, Broberg A, Röhnisch HE. Extended automated quantification algorithm (AQuA) for targeted 1H NMR metabolomics of highly complex samples: application to plant root exudates. Metabolomics 2023; 20:11. [PMID: 38141081 DOI: 10.1007/s11306-023-02073-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
INTRODUCTION The Automated Quantification Algorithm (AQuA) is a rapid and efficient method for targeted NMR-based metabolomics, currently optimised for blood plasma. AQuA quantifies metabolites from 1D-1H NMR spectra based on the height of only one signal per metabolite, which minimises the computational time and workload of the method without compromising the quantification accuracy. OBJECTIVES To develop a fast and computationally efficient extension of AQuA for quantification of selected metabolites in highly complex samples, with minimal prior sample preparation. In particular, the method should be capable of handling interferences caused by broad background signals. METHODS An automatic baseline correction function was combined with AQuA into an automated workflow, the extended AQuA, for quantification of metabolites in plant root exudate NMR spectra that contained broad background signals and baseline distortions. The approach was evaluated using simulations as well as a spike-in experiment in which known metabolite amounts were added to a complex sample matrix. RESULTS The extended AQuA enables accurate quantification of metabolites in 1D-1H NMR spectra with varying complexity. The method is very fast (< 1 s per spectrum) and can be fully automated. CONCLUSIONS The extended AQuA is an automated quantification method intended for 1D-1H NMR spectra containing broad background signals and baseline distortions. Although the method was developed for plant root exudates, it should be readily applicable to any NMR spectra displaying similar issues as it is purely computational and applied to NMR spectra post-acquisition.
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Affiliation(s)
- Elin Alexandersson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Corine Sandström
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Meijer
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gustav Nestor
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hanna E Röhnisch
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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3
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Rout M, Lipfert M, Lee BL, Berjanskii M, Assempour N, Fresno RV, Cayuela AS, Dong Y, Johnson M, Shahin H, Gautam V, Sajed T, Oler E, Peters H, Mandal R, Wishart DS. MagMet: A fully automated web server for targeted nuclear magnetic resonance metabolomics of plasma and serum. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:681-704. [PMID: 37265034 DOI: 10.1002/mrc.5371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectral analysis of biofluids can be a time-consuming process, requiring the expertise of a trained operator. With NMR becoming increasingly popular in the field of metabolomics, there is a growing need to change this paradigm and to automate the process. Here we introduce MagMet, an online web server, that automates the processing and quantification of 1D 1 H NMR spectra from biofluids-specifically, human serum/plasma metabolites, including those associated with inborn errors of metabolism (IEM). MagMet uses a highly efficient data processing procedure that performs automatic Fourier Transformation, phase correction, baseline optimization, chemical shift referencing, water signal removal, and peak picking/peak alignment. MagMet then uses the peak positions, linewidth information, and J-couplings from its own specially prepared standard metabolite reference spectral NMR library of 85 serum/plasma compounds to identify and quantify compounds from experimentally acquired NMR spectra of serum/plasma. MagMet employs linewidth adjustment for more consistent quantification of metabolites from higher field instruments and incorporates a highly efficient data processing procedure for more rapid and accurate detection and quantification of metabolites. This optimized algorithm allows the MagMet webserver to quickly detect and quantify 58 serum/plasma metabolites in 2.6 min per spectrum (when processing a dataset of 50-100 spectra). MagMet's performance was also assessed using spectra collected from defined mixtures (simulating other biofluids), with >100 previously measured plasma spectra, and from spiked serum/plasma samples simulating known IEMs. In all cases, MagMet performed with precision and accuracy matching the performance of human spectral profiling experts. MagMet is available at http://magmet.ca.
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Affiliation(s)
- Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Matthias Lipfert
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mark Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nazanin Assempour
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rosa Vazquez Fresno
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Arnau Serra Cayuela
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ying Dong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mathew Johnson
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Honeya Shahin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tanvir Sajed
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Harrison Peters
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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4
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Zou X, Liu Y, Wang M, Zou J, Shi Y, Su X, Xu J, Tong HHY, Ji Y, Gui L, Hao J. scCURE identifies cell types responding to immunotherapy and enables outcome prediction. CELL REPORTS METHODS 2023; 3:100643. [PMID: 37989083 PMCID: PMC10694528 DOI: 10.1016/j.crmeth.2023.100643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
A deep understanding of immunotherapy response/resistance mechanisms and a highly reliable therapy response prediction are vital for cancer treatment. Here, we developed scCURE (single-cell RNA sequencing [scRNA-seq] data-based Changed and Unchanged cell Recognition during immunotherapy). Based on Gaussian mixture modeling, Kullback-Leibler (KL) divergence, and mutual nearest-neighbors criteria, scCURE can faithfully discriminate between cells affected or unaffected by immunotherapy intervention. By conducting scCURE analyses in melanoma and breast cancer immunotherapy scRNA-seq data, we found that the baseline profiles of specific CD8+ T and macrophage cells (identified by scCURE) can determine the way in which tumor microenvironment immune cells respond to immunotherapy, e.g., antitumor immunity activation or de-activation; therefore, these cells could be predictive factors for treatment response. In this work, we demonstrated that the immunotherapy-associated cell-cell heterogeneities revealed by scCURE can be utilized to integrate the therapy response mechanism study and prediction model construction.
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Affiliation(s)
- Xin Zou
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai 201508, China; Department of Pathology, Jinshan Hospital, Fudan University, Shanghai 201508, China.
| | - Yujun Liu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Miaochen Wang
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiawei Zou
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Xianbin Su
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai, China
| | - Juan Xu
- Department of Stomatology, Sijing Hospital, Shanghai 201601, China
| | - Henry H Y Tong
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, China
| | - Yuan Ji
- Molecular Pathology Center, Department Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lv Gui
- Department of Pathology, Jinshan Hospital, Fudan University, Shanghai 201508, China.
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
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5
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Shastry A, Dunham-Snary K. Metabolomics and mitochondrial dysfunction in cardiometabolic disease. Life Sci 2023; 333:122137. [PMID: 37788764 DOI: 10.1016/j.lfs.2023.122137] [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: 08/01/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
Circulating metabolites are indicators of systemic metabolic dysfunction and can be detected through contemporary techniques in metabolomics. These metabolites are involved in numerous mitochondrial metabolic processes including glycolysis, fatty acid β-oxidation, and amino acid catabolism, and changes in the abundance of these metabolites is implicated in the pathogenesis of cardiometabolic diseases (CMDs). Epigenetic regulation and direct metabolite-protein interactions modulate metabolism, both within cells and in the circulation. Dysfunction of multiple mitochondrial components stemming from mitochondrial DNA mutations are implicated in disease pathogenesis. This review will summarize the current state of knowledge regarding: i) the interactions between metabolites found within the mitochondrial environment during CMDs, ii) various metabolites' effects on cellular and systemic function, iii) how harnessing the power of metabolomic analyses represents the next frontier of precision medicine, and iv) how these concepts integrate to expand the clinical potential for translational cardiometabolic medicine.
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Affiliation(s)
- Abhishek Shastry
- Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Kimberly Dunham-Snary
- Department of Medicine, Queen's University, Kingston, ON, Canada; Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON, Canada.
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6
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Han X, Wang W, Ma LH, AI-Ramahi I, Botas J, MacKenzie K, Allen GI, Young DW, Liu Z, Maletic-Savatic M. SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra. Bioinformatics 2023; 39:btad593. [PMID: 37792497 PMCID: PMC10568371 DOI: 10.1093/bioinformatics/btad593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/31/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023] Open
Abstract
MOTIVATION Nuclear magnetic resonance spectroscopy (NMR) is widely used to analyze metabolites in biological samples, but the analysis requires specific expertise, it is time-consuming, and can be inaccurate. Here, we present a powerful automate tool, SPatial clustering Algorithm-Statistical TOtal Correlation SpectroscopY (SPA-STOCSY), which overcomes challenges faced when analyzing NMR data and identifies metabolites in a sample with high accuracy. RESULTS As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset. It first investigates the covariance pattern among datapoints and then calculates the optimal threshold with which to cluster datapoints belonging to the same structural unit, i.e. the metabolite. Generated clusters are then automatically linked to a metabolite library to identify candidates. To assess SPA-STOCSY's efficiency and accuracy, we applied it to synthesized spectra and spectra acquired on Drosophila melanogaster tissue and human embryonic stem cells. In the synthesized spectra, SPA outperformed Statistical Recoupling of Variables (SRV), an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the biological data, SPA-STOCSY performed comparably to the operator-based Chenomx analysis while avoiding operator bias, and it required <7 min of total computation time. Overall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. It may thus accelerate the use of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making. AVAILABILITY AND IMPLEMENTATION The codes of SPA-STOCSY are available at https://github.com/LiuzLab/SPA-STOCSY.
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Affiliation(s)
- Xu Han
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Wanli Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Graduate Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, United States
| | - Li-Hua Ma
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, United States
| | - Ismael AI-Ramahi
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, United States
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, United States
| | - Kevin MacKenzie
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, United States
| | - Genevera I Allen
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Electrical and Computer Engineering, Statistics, and Computer Science, Rice University, Houston, TX 77005-1827, United States
| | - Damian W Young
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, United States
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mirjana Maletic-Savatic
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX 77030, United States
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7
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Alonso-Moreno P, Rodriguez I, Izquierdo-Garcia JL. Benchtop NMR-Based Metabolomics: First Steps for Biomedical Application. Metabolites 2023; 13:metabo13050614. [PMID: 37233655 DOI: 10.3390/metabo13050614] [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: 12/30/2022] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics is a valuable tool for identifying biomarkers and understanding the underlying metabolic changes associated with various diseases. However, the translation of metabolomics analysis to clinical practice has been limited by the high cost and large size of traditional high-resolution NMR spectrometers. Benchtop NMR, a compact and low-cost alternative, offers the potential to overcome these limitations and facilitate the wider use of NMR-based metabolomics in clinical settings. This review summarizes the current state of benchtop NMR for clinical applications where benchtop NMR has demonstrated the ability to reproducibly detect changes in metabolite levels associated with diseases such as type 2 diabetes and tuberculosis. Benchtop NMR has been used to identify metabolic biomarkers in a range of biofluids, including urine, blood plasma and saliva. However, further research is needed to optimize the use of benchtop NMR for clinical applications and to identify additional biomarkers that can be used to monitor and manage a range of diseases. Overall, benchtop NMR has the potential to revolutionize the way metabolomics is used in clinical practice, providing a more accessible and cost-effective way to study metabolism and identify biomarkers for disease diagnosis, prognosis, and treatment.
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Affiliation(s)
- Pilar Alonso-Moreno
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ignacio Rodriguez
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Chemistry in Pharmaceutical Sciences, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jose Luis Izquierdo-Garcia
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Chemistry in Pharmaceutical Sciences, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
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8
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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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9
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Han X, Wang W, Ma LH, Al-Ramahi I, Botas J, MacKenzie K, Allen GI, Young DW, Liu Z, Maletic-Savatic M. SPA-STOCSY: An Automated Tool for Identification of Annotated and Non-Annotated Metabolites in High-Throughput NMR Spectra. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529564. [PMID: 36865102 PMCID: PMC9980041 DOI: 10.1101/2023.02.22.529564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is widely used to analyze metabolites in biological samples, but the analysis can be cumbersome and inaccurate. Here, we present a powerful automated tool, SPA-STOCSY (Spatial Clustering Algorithm - Statistical Total Correlation Spectroscopy), which overcomes the challenges by identifying metabolites in each sample with high accuracy. As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset, first investigating the covariance pattern and then calculating the optimal threshold with which to cluster data points belonging to the same structural unit, i.e. metabolite. The generated clusters are then automatically linked to a compound library to identify candidates. To assess SPA-STOCSY’s efficiency and accuracy, we applied it to synthesized and real NMR data obtained from Drosophila melanogaster brains and human embryonic stem cells. In the synthesized spectra, SPA outperforms Statistical Recoupling of Variables, an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the real spectra, SPA-STOCSY performs comparably to operator-based Chenomx analysis but avoids operator bias and performs the analyses in less than seven minutes of total computation time. Overall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. As such, it might accelerate the utilization of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making.
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Affiliation(s)
- Xu Han
- 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
| | - 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
| | - Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin MacKenzie
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Department of Pathology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Genevera I. Allen
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005-1827, USA
| | - Damian W. Young
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, 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
| | - 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
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10
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de Medeiros LS, de Araújo Júnior MB, Peres EG, da Silva JCI, Bassicheto MC, Di Gioia G, Veiga TAM, Koolen HHF. Discovering New Natural Products Using Metabolomics-Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:185-224. [PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.
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Affiliation(s)
- Lívia Soman de Medeiros
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil.
| | - Moysés B de Araújo Júnior
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eldrinei G Peres
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | | | - Milena Costa Bassicheto
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Giordanno Di Gioia
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Thiago André Moura Veiga
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
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11
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Affiliation(s)
- Rustam Aminov
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
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12
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Bliziotis NG, Kluijtmans LAJ, Tinnevelt GH, Reel P, Reel S, Langton K, Robledo M, Pamporaki C, Pecori A, Van Kralingen J, Tetti M, Engelke UFH, Erlic Z, Engel J, Deutschbein T, Nölting S, Prejbisz A, Richter S, Adamski J, Januszewicz A, Ceccato F, Scaroni C, Dennedy MC, Williams TA, Lenzini L, Gimenez-Roqueplo AP, Davies E, Fassnacht M, Remde H, Eisenhofer G, Beuschlein F, Kroiss M, Jefferson E, Zennaro MC, Wevers RA, Jansen JJ, Deinum J, Timmers HJLM. Preanalytical Pitfalls in Untargeted Plasma Nuclear Magnetic Resonance Metabolomics of Endocrine Hypertension. Metabolites 2022; 12:metabo12080679. [PMID: 35893246 PMCID: PMC9394285 DOI: 10.3390/metabo12080679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/17/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
Despite considerable morbidity and mortality, numerous cases of endocrine hypertension (EHT) forms, including primary aldosteronism (PA), pheochromocytoma and functional paraganglioma (PPGL), and Cushing’s syndrome (CS), remain undetected. We aimed to establish signatures for the different forms of EHT, investigate potentially confounding effects and establish unbiased disease biomarkers. Plasma samples were obtained from 13 biobanks across seven countries and analyzed using untargeted NMR metabolomics. We compared unstratified samples of 106 PHT patients to 231 EHT patients, including 104 PA, 94 PPGL and 33 CS patients. Spectra were subjected to a multivariate statistical comparison of PHT to EHT forms and the associated signatures were obtained. Three approaches were applied to investigate and correct confounding effects. Though we found signatures that could separate PHT from EHT forms, there were also key similarities with the signatures of sample center of origin and sample age. The study design restricted the applicability of the corrections employed. With the samples that were available, no biomarkers for PHT vs. EHT could be identified. The complexity of the confounding effects, evidenced by their robustness to correction approaches, highlighted the need for a consensus on how to deal with variabilities probably attributed to preanalytical factors in retrospective, multicenter metabolomics studies.
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Affiliation(s)
- Nikolaos G. Bliziotis
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Correspondence: (N.G.B.); (L.A.J.K.); (R.A.W.); (H.J.L.M.T.)
| | - Leo A. J. Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Correspondence: (N.G.B.); (L.A.J.K.); (R.A.W.); (H.J.L.M.T.)
| | - Gerjen H. Tinnevelt
- Department of Analytical Chemistry, Institute for Molecules and Materials, Radboud University, 6500 HB Nijmegen, The Netherlands; (G.H.T.); (J.J.J.)
| | - Parminder Reel
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee DD2 4BF, UK; (P.R.); (S.R.); (E.J.)
| | - Smarti Reel
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee DD2 4BF, UK; (P.R.); (S.R.); (E.J.)
| | - Katharina Langton
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.L.); (C.P.); (G.E.)
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
| | - Christina Pamporaki
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.L.); (C.P.); (G.E.)
| | - Alessio Pecori
- Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, 10124 Torino, Italy; (A.P.); (M.T.); (T.A.W.)
| | - Josie Van Kralingen
- British Heart Foundation Glasgow Cardiovascular Research Centre (BHF GCRC), Institute of Cardiovascular & Medical Sciences (ICAMS), University of Glasgow, Glasgow G12 8TA, UK; (J.V.K.); (E.D.)
| | - Martina Tetti
- Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, 10124 Torino, Italy; (A.P.); (M.T.); (T.A.W.)
| | - Udo F. H. Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Zoran Erlic
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ), University of Zurich (UZH), 8006 Zurich, Switzerland; (Z.E.); (F.B.)
| | - Jasper Engel
- Biometris, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
| | - Timo Deutschbein
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
- Medicover Oldenburg MVZ, 26122 Oldenburg, Germany
| | - Svenja Nölting
- Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany;
| | - Aleksander Prejbisz
- Department of Hypertension, Institute of Cardiology, 04-628 Warsaw, Poland; (A.P.); (A.J.)
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany;
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Center München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Experimental Genetics, Technical University München, 85350 Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077 Singapore, Singapore
| | - Andrzej Januszewicz
- Department of Hypertension, Institute of Cardiology, 04-628 Warsaw, Poland; (A.P.); (A.J.)
| | - Filippo Ceccato
- Endocrinology Unit, Department of Medicine DIMED, University-Hospital of Padova, 35128 Padova, Italy; (F.C.); (C.S.)
| | - Carla Scaroni
- Endocrinology Unit, Department of Medicine DIMED, University-Hospital of Padova, 35128 Padova, Italy; (F.C.); (C.S.)
| | - Michael C. Dennedy
- The Discipline of Pharmacology and Therapeutics, School of Medicine, National University of Ireland, H91 CF50 Galway, Ireland;
| | - Tracy A. Williams
- Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, 10124 Torino, Italy; (A.P.); (M.T.); (T.A.W.)
| | - Livia Lenzini
- Department of Medicine-DIMED, Emergency and Hypertension Unit, University of Padova, University Hospital, 35126 Padova, Italy;
| | - Anne-Paule Gimenez-Roqueplo
- INSERM, PARCC, Université de Paris, 75015 Paris, France; (A.-P.G.-R.); (M.-C.Z.)
- Service de Genétique, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Eleanor Davies
- British Heart Foundation Glasgow Cardiovascular Research Centre (BHF GCRC), Institute of Cardiovascular & Medical Sciences (ICAMS), University of Glasgow, Glasgow G12 8TA, UK; (J.V.K.); (E.D.)
| | - Martin Fassnacht
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
- Core Unit Clinical Mass Spectrometry, University Hospital Würzburg, 97080 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg University, 97070 Würzburg, Germany
| | - Hanna Remde
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
| | - Graeme Eisenhofer
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.L.); (C.P.); (G.E.)
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany;
| | - Felix Beuschlein
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ), University of Zurich (UZH), 8006 Zurich, Switzerland; (Z.E.); (F.B.)
- Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany;
| | - Matthias Kroiss
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
- Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany;
- Core Unit Clinical Mass Spectrometry, University Hospital Würzburg, 97080 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg University, 97070 Würzburg, Germany
| | - Emily Jefferson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee DD2 4BF, UK; (P.R.); (S.R.); (E.J.)
- Institute of Health & Wellbeing, Glasgow University, Glasgow G12 8RZ, UK
| | - Maria-Christina Zennaro
- INSERM, PARCC, Université de Paris, 75015 Paris, France; (A.-P.G.-R.); (M.-C.Z.)
- Service de Genétique, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Ron A. Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Correspondence: (N.G.B.); (L.A.J.K.); (R.A.W.); (H.J.L.M.T.)
| | - Jeroen J. Jansen
- Department of Analytical Chemistry, Institute for Molecules and Materials, Radboud University, 6500 HB Nijmegen, The Netherlands; (G.H.T.); (J.J.J.)
| | - Jaap Deinum
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Henri J. L. M. Timmers
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Correspondence: (N.G.B.); (L.A.J.K.); (R.A.W.); (H.J.L.M.T.)
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13
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Wang X, Mickiewicz B, Thompson GC, Joffe AR, Blackwood J, Vogel HJ, Kopciuk KA. Comparison of Two Automated Targeted Metabolomics Programs to Manual Profiling by an Experienced Spectroscopist for 1H-NMR Spectra. Metabolites 2022; 12:metabo12030227. [PMID: 35323670 PMCID: PMC8949809 DOI: 10.3390/metabo12030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 12/10/2022] Open
Abstract
Automated programs that carry out targeted metabolite identification and quantification using proton nuclear magnetic resonance spectra can overcome time and cost barriers that limit metabolomics use. However, their performance needs to be comparable to that of an experienced spectroscopist. A previously analyzed pediatric sepsis data set of serum samples was used to compare results generated by the automated programs rDolphin and BATMAN with the results obtained by manual profiling for 58 identified metabolites. Metabolites were selected using Student’s t-tests and evaluated with several performance metrics. The manual profiling results had the highest performance metrics values, especially for sensitivity (76.9%), area under the receiver operating characteristic curve (0.90), precision (62.5%), and testing accuracy based on a neural net (88.6%). All three approaches had high specificity values (77.7–86.7%). Manual profiling by an expert spectroscopist outperformed two open-source automated programs, indicating that further development is needed to achieve acceptable performance levels.
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Affiliation(s)
- Xiangyu Wang
- Department of Mathematics and Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Beata Mickiewicz
- Department of Pediatrics, Cumming School of Medicine and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Graham C. Thompson
- Departments of Pediatrics and Emergency Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Ari R. Joffe
- Department of Pediatrics, Division of Pediatric Critical Care, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Jaime Blackwood
- Department of PICU and Critical Care, Alberta Children’s Hospital, Alberta Health Services, Calgary, AB T3B 6A8, Canada;
| | - Hans J. Vogel
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB T2N 1N4, Canada
- Correspondence:
| | - Karen A. Kopciuk
- Departments of Community Health Sciences, Mathematics and Statistics, and Oncology, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Cancer Epidemiology and Prevention Research, Alberta Health Sciences, Calgary, AB T2S 3C3, Canada
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14
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Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part I: Emerging Platforms and Perspectives. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
1H NMR-based metabolomics analysis of human saliva, other oral fluids, and/or tissue biopsies serves as a valuable technique for the exploration of metabolic processes, and when associated with ’state-of-the-art’ multivariate (MV) statistical analysis strategies, provides a powerful means of examining the identification of characteristic metabolite patterns, which may serve to differentiate between patients with oral health conditions (e.g., periodontitis, dental caries, and oral cancers) and age-matched heathy controls. This approach may also be employed to explore such discriminatory signatures in the salivary 1H NMR profiles of patients with systemic diseases, and to date, these have included diabetes, Sjörgen’s syndrome, cancers, neurological conditions such as Alzheimer’s disease, and viral infections. However, such investigations are complicated in view of quite a large number of serious inconsistencies between the different studies performed by independent research groups globally; these include differing protocols and routes for saliva sample collection (e.g., stimulated versus unstimulated samples), their timings (particularly the oral activity abstention period involved, which may range from one to 12 h or more), and methods for sample transport, storage, and preparation for NMR analysis, not to mention a very wide variety of demographic variables that may influence salivary metabolite concentrations, notably the age, gender, ethnic origin, salivary flow-rate, lifestyles, diets, and smoking status of participant donors, together with their exposure to any other possible convoluting environmental factors. In view of the explosive increase in reported salivary metabolomics investigations, in this update, we critically review a wide range of critical considerations for the successful performance of such experiments. These include the nature, composite sources, and biomolecular status of human saliva samples; the merits of these samples as media for the screening of disease biomarkers, notably their facile, unsupervised collection; and the different classes of such metabolomics investigations possible. Also encompassed is an account of the history of NMR-based salivary metabolomics; our recommended regimens for the collection, transport, and storage of saliva samples, along with their preparation for NMR analysis; frequently employed pulse sequences for the NMR analysis of these samples; the supreme resonance assignment benefits offered by homo- and heteronuclear two-dimensional NMR techniques; deliberations regarding salivary biomolecule quantification approaches employed for such studies, including the preprocessing and bucketing of multianalyte salivary NMR spectra, and the normalization, transformation, and scaling of datasets therefrom; salivary phenotype analysis, featuring the segregation of a range of different metabolites into ‘pools’ grouped according to their potential physiological sources; and lastly, future prospects afforded by the applications of LF benchtop NMR spectrometers for direct evaluations of the oral or systemic health status of patients at clinical ‘point-of-contact’ sites, e.g., dental surgeries. This commentary is then concluded with appropriate recommendations for the conduct of future salivary metabolomics studies. Also included are two original case studies featuring investigations of (1) the 1H NMR resonance line-widths of selected biomolecules and their possible dependence on biomacromolecular binding equilibria, and (2) the combined univariate (UV) and MV analysis of saliva specimens collected from a large group of healthy control participants in order to potentially delineate the possible origins of biomolecules therein, particularly host- versus oral microbiome-derived sources. In a follow-up publication, Part II of this series, we conduct censorious reviews of reported observations acquired from a diversity of salivary metabolomics investigations performed to evaluate both localized oral and non-oral diseases. Perplexing problems encountered with these again include those arising from sample collection and preparation protocols, along with 1H NMR spectral misassignments.
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15
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Caudai C, Galizia A, Geraci F, Le Pera L, Morea V, Salerno E, Via A, Colombo T. AI applications in functional genomics. Comput Struct Biotechnol J 2021; 19:5762-5790. [PMID: 34765093 PMCID: PMC8566780 DOI: 10.1016/j.csbj.2021.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
We review the current applications of artificial intelligence (AI) in functional genomics. The recent explosion of AI follows the remarkable achievements made possible by "deep learning", along with a burst of "big data" that can meet its hunger. Biology is about to overthrow astronomy as the paradigmatic representative of big data producer. This has been made possible by huge advancements in the field of high throughput technologies, applied to determine how the individual components of a biological system work together to accomplish different processes. The disciplines contributing to this bulk of data are collectively known as functional genomics. They consist in studies of: i) the information contained in the DNA (genomics); ii) the modifications that DNA can reversibly undergo (epigenomics); iii) the RNA transcripts originated by a genome (transcriptomics); iv) the ensemble of chemical modifications decorating different types of RNA transcripts (epitranscriptomics); v) the products of protein-coding transcripts (proteomics); and vi) the small molecules produced from cell metabolism (metabolomics) present in an organism or system at a given time, in physiological or pathological conditions. After reviewing main applications of AI in functional genomics, we discuss important accompanying issues, including ethical, legal and economic issues and the importance of explainability.
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Affiliation(s)
- Claudia Caudai
- CNR, Institute of Information Science and Technologies “A. Faedo” (ISTI), Pisa, Italy
| | - Antonella Galizia
- CNR, Institute of Applied Mathematics and Information Technologies (IMATI), Genoa, Italy
| | - Filippo Geraci
- CNR, Institute for Informatics and Telematics (IIT), Pisa, Italy
| | - Loredana Le Pera
- CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
| | - Veronica Morea
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
| | - Emanuele Salerno
- CNR, Institute of Information Science and Technologies “A. Faedo” (ISTI), Pisa, Italy
| | - Allegra Via
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
| | - Teresa Colombo
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
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Letertre MPM, Giraudeau P, de Tullio P. Nuclear Magnetic Resonance Spectroscopy in Clinical Metabolomics and Personalized Medicine: Current Challenges and Perspectives. Front Mol Biosci 2021; 8:698337. [PMID: 34616770 PMCID: PMC8488110 DOI: 10.3389/fmolb.2021.698337] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is probably the most promising area being developed in modern medicine. This approach attempts to optimize the therapies and the patient care based on the individual patient characteristics. Its success highly depends on the way the characterization of the disease and its evolution, the patient’s classification, its follow-up and the treatment could be optimized. Thus, personalized medicine must combine innovative tools to measure, integrate and model data. Towards this goal, clinical metabolomics appears as ideally suited to obtain relevant information. Indeed, the metabolomics signature brings crucial insight to stratify patients according to their responses to a pathology and/or a treatment, to provide prognostic and diagnostic biomarkers, and to improve therapeutic outcomes. However, the translation of metabolomics from laboratory studies to clinical practice remains a subsequent challenge. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are the two key platforms for the measurement of the metabolome. NMR has several advantages and features that are essential in clinical metabolomics. Indeed, NMR spectroscopy is inherently very robust, reproducible, unbiased, quantitative, informative at the structural molecular level, requires little sample preparation and reduced data processing. NMR is also well adapted to the measurement of large cohorts, to multi-sites and to longitudinal studies. This review focus on the potential of NMR in the context of clinical metabolomics and personalized medicine. Starting with the current status of NMR-based metabolomics at the clinical level and highlighting its strengths, weaknesses and challenges, this article also explores how, far from the initial “opposition” or “competition”, NMR and MS have been integrated and have demonstrated a great complementarity, in terms of sample classification and biomarker identification. Finally, a perspective discussion provides insight into the current methodological developments that could significantly raise NMR as a more resolutive, sensitive and accessible tool for clinical applications and point-of-care diagnosis. Thanks to these advances, NMR has a strong potential to join the other analytical tools currently used in clinical settings.
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Affiliation(s)
| | | | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research of Medicine (CIRM), Department of Pharmacy, Université de Liège, Liège, Belgique
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17
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Statistical analysis in metabolic phenotyping. Nat Protoc 2021; 16:4299-4326. [PMID: 34321638 DOI: 10.1038/s41596-021-00579-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/27/2021] [Indexed: 01/09/2023]
Abstract
Metabolic phenotyping is an important tool in translational biomedical research. The advanced analytical technologies commonly used for phenotyping, including mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy, generate complex data requiring tailored statistical analysis methods. Detailed protocols have been published for data acquisition by liquid NMR, solid-state NMR, ultra-performance liquid chromatography (LC-)MS and gas chromatography (GC-)MS on biofluids or tissues and their preprocessing. Here we propose an efficient protocol (guidelines and software) for statistical analysis of metabolic data generated by these methods. Code for all steps is provided, and no prior coding skill is necessary. We offer efficient solutions for the different steps required within the complete phenotyping data analytics workflow: scaling, normalization, outlier detection, multivariate analysis to explore and model study-related effects, selection of candidate biomarkers, validation, multiple testing correction and performance evaluation of statistical models. We also provide a statistical power calculation algorithm and safeguards to ensure robust and meaningful experimental designs that deliver reliable results. We exemplify the protocol with a two-group classification study and data from an epidemiological cohort; however, the protocol can be easily modified to cover a wider range of experimental designs or incorporate different modeling approaches. This protocol describes a minimal set of analyses needed to rigorously investigate typical datasets encountered in metabolic phenotyping.
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18
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Schultheiss UT, Kosch R, Kotsis F, Altenbuchinger M, Zacharias HU. Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses. Metabolites 2021; 11:460. [PMID: 34357354 PMCID: PMC8304377 DOI: 10.3390/metabo11070460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Kidney diseases still pose one of the biggest challenges for global health, and their heterogeneity and often high comorbidity load seriously hinders the unraveling of their underlying pathomechanisms and the delivery of optimal patient care. Metabolomics, the quantitative study of small organic compounds, called metabolites, in a biological specimen, is gaining more and more importance in nephrology research. Conducting a metabolomics study in human kidney disease cohorts, however, requires thorough knowledge about the key workflow steps: study planning, sample collection, metabolomics data acquisition and preprocessing, statistical/bioinformatics data analysis, and results interpretation within a biomedical context. This review provides a guide for future metabolomics studies in human kidney disease cohorts. We will offer an overview of important a priori considerations for metabolomics cohort studies, available analytical as well as statistical/bioinformatics data analysis techniques, and subsequent interpretation of metabolic findings. We will further point out potential research questions for metabolomics studies in the context of kidney diseases and summarize the main results and data availability of important studies already conducted in this field.
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Affiliation(s)
- Ulla T. Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany; (U.T.S.); (F.K.)
- Department of Medicine IV—Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Robin Kosch
- Computational Biology, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany; (U.T.S.); (F.K.)
- Department of Medicine IV—Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Michael Altenbuchinger
- Institute of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany;
| | - Helena U. Zacharias
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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19
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An R-Package for the Deconvolution and Integration of 1D NMR Data: MetaboDecon1D. Metabolites 2021; 11:metabo11070452. [PMID: 34357346 PMCID: PMC8305572 DOI: 10.3390/metabo11070452] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/03/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022] Open
Abstract
NMR spectroscopy is a widely used method for the detection and quantification of metabolites in complex biological fluids. However, the large number of metabolites present in a biological sample such as urine or plasma leads to considerable signal overlap in one-dimensional NMR spectra, which in turn hampers both signal identification and quantification. As a consequence, we have developed an easy to use R-package that allows the fully automated deconvolution of overlapping signals in the underlying Lorentzian line-shapes. We show that precise integral values are computed, which are required to obtain both relative and absolute quantitative information. The algorithm is independent of any knowledge of the corresponding metabolites, which also allows the quantitative description of features of yet unknown identity.
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20
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Data Processing Optimization in Untargeted Metabolomics of Urine Using Voigt Lineshape Model Non-Linear Regression Analysis. Metabolites 2021; 11:metabo11050285. [PMID: 33947160 PMCID: PMC8145719 DOI: 10.3390/metabo11050285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is well-established to address questions in large-scale untargeted metabolomics. Although several approaches in data processing and analysis are available, significant issues remain. NMR spectroscopy of urine generates information-rich but complex spectra in which signals often overlap. Furthermore, slight changes in pH and salt concentrations cause peak shifting, which introduces, in combination with baseline irregularities, un-informative noise in statistical analysis. Within this work, a straight-forward data processing tool addresses these problems by applying a non-linear curve fitting model based on Voigt function line shape and integration of the underlying peak areas. This method allows a rapid untargeted analysis of urine metabolomics datasets without relying on time-consuming 2D-spectra based deconvolution or information from spectral libraries. The approach is validated with spiking experiments and tested on a human urine 1H dataset compared to conventionally used methods and aims to facilitate metabolomics data analysis.
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21
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Cardoso S, Cabral D, Maraschin M, Rocha M. NMRFinder: a novel method for 1D 1H-NMR metabolite annotation. Metabolomics 2021; 17:21. [PMID: 33523311 DOI: 10.1007/s11306-021-01772-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/20/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Methods for the automated and accurate identification of metabolites in 1D 1H-NMR samples are crucial, but this is still an unsolved problem. Most available tools are mainly focused on metabolite quantification, thus limiting the number of metabolites that can be identified. Also, most only use reference spectra obtained under the same specific conditions of the target sample, limiting the use of available knowledge. OBJECTIVES The main goal of this work was to develop novel methods to perform metabolite annotation from 1D 1H-NMR peaks with enhanced reliability, to aid the users in metabolite identification. An essential step was to construct a vast and up-do-date library of reference 1D 1H-NMR peak lists collected under distinct experimental conditions. METHODS Three different algorithms were evaluated for their capacity to correctly annotate metabolites present in both synthetic and real samples and compared to publicly available tools. The best proposed method was evaluated in a plethora of scenarios, including missing references, missing peaks and peak shifts, to assess its annotation accuracy, precision and recall. RESULTS We gathered 1816 peak lists for 1387 different metabolites from several sources across different conditions for our reference library. A new method, NMRFinder, is proposed and allows matching 1D 1H-NMR samples with all the reference peak lists in the library, regardless of acquisition conditions. Metabolites are scored according to the number of peaks matching the samples, how unique their peaks are in the library and how close the spectrum acquisition conditions are in relation to those of the samples. Results show a true positive rate of 0.984 when analysing computationally created samples, while 71.8% of the metabolites were annotated when analysing samples from previously identified public datasets. CONCLUSION NMRFinder performs metabolite annotation reliably and outperforms previous methods, being of great value in helping the user to ultimately identify metabolites. It is implemented in the R package specmine.
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Affiliation(s)
- Sara Cardoso
- CEB-Centre Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
| | - Débora Cabral
- Plant Morphogenesis and Biochemistry Laboratory, Federal University of Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Marcelo Maraschin
- Plant Morphogenesis and Biochemistry Laboratory, Federal University of Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Miguel Rocha
- CEB-Centre Biological Engineering, University of Minho, 4710-057, Braga, Portugal
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22
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Solovyev PA, Fauhl-Hassek C, Riedl J, Esslinger S, Bontempo L, Camin F. NMR spectroscopy in wine authentication: An official control perspective. Compr Rev Food Sci Food Saf 2021; 20:2040-2062. [PMID: 33506593 DOI: 10.1111/1541-4337.12700] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/30/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022]
Abstract
Wine authentication is vital in identifying malpractice and fraud, and various physical and chemical analytical techniques have been employed for this purpose. Besides wet chemistry, these include chromatography, isotopic ratio mass spectrometry, optical spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy, which have been applied in recent years in combination with chemometric approaches. For many years, 2 H NMR spectroscopy was the method of choice and achieved official recognition in the detection of sugar addition to grape products. Recently, 1 H NMR spectroscopy, a simpler and faster method (in terms of sample preparation), has gathered more and more attention in wine analysis, even if it still lacks official recognition. This technique makes targeted quantitative determination of wine ingredients and nontargeted detection of the metabolomic fingerprint of a wine sample possible. This review summarizes the possibilities and limitations of 1 H NMR spectroscopy in analytical wine authentication, by reviewing its applications as reported in the literature. Examples of commercial and open-source solutions combining NMR spectroscopy and chemometrics are also examined herein, together with its opportunities of becoming an official method.
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Affiliation(s)
- Pavel A Solovyev
- Department of Food Quality and Nutrition, Research and Innovation Center, Fondazione Edmund Mach (FEM), via E. Mach 1, San Michele all'Adige, 38010, Italy
| | - Carsten Fauhl-Hassek
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, Unit Product Identity, Supply Chains and Traceability, Max-Dohrn Strasse, 8-10, Berlin, 10589, Germany
| | - Janet Riedl
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, Unit Product Identity, Supply Chains and Traceability, Max-Dohrn Strasse, 8-10, Berlin, 10589, Germany
| | - Susanne Esslinger
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, Unit Product Identity, Supply Chains and Traceability, Max-Dohrn Strasse, 8-10, Berlin, 10589, Germany
| | - Luana Bontempo
- Department of Food Quality and Nutrition, Research and Innovation Center, Fondazione Edmund Mach (FEM), via E. Mach 1, San Michele all'Adige, 38010, Italy
| | - Federica Camin
- Department of Food Quality and Nutrition, Research and Innovation Center, Fondazione Edmund Mach (FEM), via E. Mach 1, San Michele all'Adige, 38010, Italy.,Center Agriculture Food Environment (C3A), University of Trento, via Mach 1, San Michele all'Adige, Tennessee, 38010, Italy
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23
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Kumar PR, Mishra SK, Srivastava S. Computational Metabolomics. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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24
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Crook AA, Powers R. Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications. Molecules 2020; 25:E5128. [PMID: 33158172 PMCID: PMC7662776 DOI: 10.3390/molecules25215128] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, the simple method development, minimal sample derivatization, and the simultaneous qualitative and quantitative information provide a unique landscape for biomedical metabolomics, which is not available to other techniques. Furthermore, the non-destructive nature of NMR-based metabolomics allows for multidimensional analysis of biomarkers that facilitates unambiguous assignment and quantification of metabolites in complex biofluids.
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Affiliation(s)
- Alexandra A. Crook
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA;
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA;
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
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25
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Asampille G, Cheredath A, Joseph D, Adiga SK, Atreya HS. The utility of nuclear magnetic resonance spectroscopy in assisted reproduction. Open Biol 2020; 10:200092. [PMID: 33142083 PMCID: PMC7729034 DOI: 10.1098/rsob.200092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Infertility affects approximately 15-20% of individuals of reproductive age worldwide. Over the last 40 years, assisted reproductive technology (ART) has helped millions of childless couples. However, ART is limited by a low success rate and risk of multiple gestations. Devising methods for selecting the best gamete or embryo that increases the ART success rate and prevention of multiple gestation has become one of the key goals in ART today. Special emphasis has been placed on the development of non-invasive approaches, which do not require perturbing the embryonic cells, as the current morphology-based embryo selection approach has shortcomings in predicting the implantation potential of embryos. An observed association between embryo metabolism and viability has prompted researchers to develop metabolomics-based biomarkers. Nuclear magnetic resonance (NMR) spectroscopy provides a non-invasive approach for the metabolic profiling of tissues, gametes and embryos, with the key advantage of having a minimal sample preparation procedure. Using NMR spectroscopy, biologically important molecules can be identified and quantified in intact cells, extracts or secretomes. This, in turn, helps to map out the active metabolic pathways in a system. The present review covers the contribution of NMR spectroscopy in assisted reproduction at various stages of the process.
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Affiliation(s)
- Gitanjali Asampille
- Department of Clinical Embryology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Aswathi Cheredath
- Department of Clinical Embryology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - David Joseph
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Satish K. Adiga
- Department of Clinical Embryology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
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26
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Madrid-Gambin F, Oller-Moreno S, Fernandez L, Bartova S, Giner MP, Joyce C, Ferraro F, Montoliu I, Moco S, Marco S. AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics. Bioinformatics 2020; 36:2943-2945. [PMID: 31930381 DOI: 10.1093/bioinformatics/btaa022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 12/17/2019] [Accepted: 01/10/2020] [Indexed: 12/22/2022] Open
Abstract
SUMMARY Nuclear magnetic resonance (NMR)-based metabolomics is widely used to obtain metabolic fingerprints of biological systems. While targeted workflows require previous knowledge of metabolites, prior to statistical analysis, untargeted approaches remain a challenge. Computational tools dealing with fully untargeted NMR-based metabolomics are still scarce or not user-friendly. Therefore, we developed AlpsNMR (Automated spectraL Processing System for NMR), an R package that provides automated and efficient signal processing for untargeted NMR metabolomics. AlpsNMR includes spectra loading, metadata handling, automated outlier detection, spectra alignment and peak-picking, integration and normalization. The resulting output can be used for further statistical analysis. AlpsNMR proved effective in detecting metabolite changes in a test case. The tool allows less experienced users to easily implement this workflow from spectra to a ready-to-use dataset in their routines. AVAILABILITY AND IMPLEMENTATION The AlpsNMR R package and tutorial is freely available to download from http://github.com/sipss/AlpsNMR under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Francisco Madrid-Gambin
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Sergio Oller-Moreno
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Luis Fernandez
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Department of Electronics and Biomedical Engineering, Universitat de Barcelona, Barcelona 08028, Spain
| | - Simona Bartova
- Nestlé Research, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | | | | | | | - Ivan Montoliu
- Nestlé Research, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Sofia Moco
- Nestlé Research, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Santiago Marco
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Department of Electronics and Biomedical Engineering, Universitat de Barcelona, Barcelona 08028, Spain
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27
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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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28
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Yuan B, Zhang X, Kamal GM, Jiang B, Liu M. Accurate estimation of diffusion coefficient for molecular identification in a complex background. Anal Bioanal Chem 2020; 412:4519-4525. [PMID: 32405677 DOI: 10.1007/s00216-020-02693-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 11/25/2022]
Abstract
To eliminate the effects of complex background signals and to enhance the accuracy of the diffusion coefficient measurement, derivative NMR spectroscopy with negligible loss of the spectral quality is introduced based on the customized Savitzky-Golay method and used to construct diffusion-ordered NMR spectroscopy (DOSY). The criterion of the method was established by simulations. The application of this method on mouse urine and serum showed that the accuracy and precision of diffusion coefficient measurements in a complex background were improved to enhance the identification of molecules. Graphical abstract Diffusion-ordered NMR spectroscopy is a powerful tool for analyzing complex mixtures. To improve the accuracy of diffusion coefficient measurement, the magnitude of complex derivative spectra is introduced as a post-processing method to eliminate the effects of background signals, broad signals, or distorted baseline. And thus, accurate estimate of the diffusion coefficient is ensured to enhance the molecule identification.
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Affiliation(s)
- Bin Yuan
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Ghulam Mustafa Kamal
- Department of Chemistry, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Pakistan
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
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29
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Diagnosis of Bovine Respiratory Disease in feedlot cattle using blood 1H NMR metabolomics. Sci Rep 2020; 10:115. [PMID: 31924818 PMCID: PMC6954258 DOI: 10.1038/s41598-019-56809-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022] Open
Abstract
Current diagnosis methods for Bovine Respiratory Disease (BRD) in feedlots have a low diagnostic accuracy. The current study aimed to search for blood biomarkers of BRD using 1H NMR metabolomics and determine their accuracy in diagnosing BRD. Animals with visual signs of BRD (n = 149) and visually healthy (non-BRD; n = 148) were sampled for blood metabolomics analysis. Lung lesions indicative of BRD were scored at slaughter. Non-targeted 1H NMR metabolomics was used to develop predictive algorithms for disease classification using classification and regression trees. In the absence of a gold standard for BRD diagnosis, six reference diagnosis methods were used to define an animal as BRD or non-BRD. Sensitivity (Se) and specificity (Sp) were used to estimate diagnostic accuracy (Acc). Blood metabolomics demonstrated a high accuracy at diagnosing BRD when using visual signs of BRD (Acc = 0.85), however was less accurate at diagnosing BRD using rectal temperature (Acc = 0.65), lung auscultation score (Acc = 0.61) and lung lesions at slaughter as reference diagnosis methods (Acc = 0.71). Phenylalanine, lactate, hydroxybutyrate, tyrosine, citrate and leucine were identified as metabolites of importance in classifying animals as BRD or non-BRD. The blood metabolome classified BRD and non-BRD animals with high accuracy and shows potential for use as a BRD diagnosis tool.
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30
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Graça G, Lau CHE, Gonçalves LG. Exploring Cancer Metabolism: Applications of Metabolomics and Metabolic Phenotyping in Cancer Research and Diagnostics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:367-385. [PMID: 32130709 DOI: 10.1007/978-3-030-34025-4_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Altered metabolism is one of the key hallmarks of cancer. The development of sensitive, reproducible and robust bioanalytical tools such as Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry techniques offers numerous opportunities for cancer metabolism research, and provides additional and exciting avenues in cancer diagnosis, prognosis and for the development of more effective and personalized treatments. In this chapter, we introduce the current state of the art of metabolomics and metabolic phenotyping approaches in cancer research and clinical diagnostics.
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Affiliation(s)
- Gonçalo Graça
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
| | - Chung-Ho E Lau
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Luís G Gonçalves
- Proteomics of Non-Model Organisms Lab, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Abstract
In this chapter, we summarize data preprocessing and data analysis strategies used for analysis of NMR data for metabolomics studies. Metabolomics consists of the analysis of the low molecular weight compounds in cells, tissues, or biological fluids, and has been used to reveal biomarkers for early disease detection and diagnosis, to monitor interventions, and to provide information on pathway perturbations to inform mechanisms and identifying targets. Metabolic profiling (also termed metabotyping) involves the analysis of hundreds to thousands of molecules using mainly state-of-the-art mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy technologies. While NMR is less sensitive than mass spectrometry, NMR does provide a wealth of complex and information rich metabolite data. NMR data together with the use of conventional statistics, modeling methods, and bioinformatics tools reveals biomarker and mechanistic information. A typical NMR spectrum, with up to 64k data points, of a complex biological fluid or an extract of cells and tissues consists of thousands of sharp signals that are mainly derived from small molecules. In addition, a number of advanced NMR spectroscopic methods are available for extracting information on high molecular weight compounds such as lipids or lipoproteins. There are numerous data preprocessing, data reduction, and analysis methods developed and evolving in the field of NMR metabolomics. Our goal is to provide an extensive summary of NMR data preprocessing and analysis strategies by providing examples and open source and commercially available analysis software and bioinformatics tools.
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Affiliation(s)
- Wimal Pathmasiri
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA.
| | - Kristine Kay
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan McRitchie
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan Sumner
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
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32
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Sengupta A, Weljie AM. NMR Spectroscopy-Based Metabolic Profiling of Biospecimens. ACTA ACUST UNITED AC 2019; 98:e98. [PMID: 31763785 DOI: 10.1002/cpps.98] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics refers to study of metabolites in biospecimens such as blood serum, tissues, and urine. Nuclear magnetic resonance (NMR) spectroscopy and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS; mass spectrometry coupled with liquid chromatography) are most frequently employed to analyze complex biological/clinical samples. NMR is a relatively insensitive tool compared to UPLC-MS/MS but offers straightforward quantification and identification and easy sample processing. One-dimensional 1 H NMR spectroscopy is inherently quantitative and can be readily used for metabolite quantification without individual metabolite standards. Two-dimensional spectroscopy is most commonly used for identification of metabolites but can also be used quantitatively. Although NMR experiments are unbiased regarding the chemical nature of the analyte, it is crucial to adhere to the proper metabolite extraction protocol for optimum results. Selection and implementation of appropriate NMR pulse programs are also important. Finally, employment of the correct metabolite quantification strategy is crucial as well. In this unit, step-by-step guidance for running an NMR metabolomics experiment from typical biospecimens is presented. The unit describes an optimized metabolite extraction protocol, followed by implementation of NMR experiments and quantification strategies using the so-called "targeted profiling" technique. This approach relies on an underlying basis set of metabolite spectra acquired under similar conditions. Some strategies for statistical analysis of the data are also presented. Overall, this set of protocols should serve as a guide for anyone who wishes to enter the world of NMR-based metabolomics analysis. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Metabolite extraction from different biospecimens Basic Protocol 2: Preparation of dried upper fraction for NMR analysis Alternate Protocol: Preparation of urine samples for NMR analysis Basic Protocol 3: NMR experiments Basic Protocol 4: Spectral processing and quantification of metabolites Basic Protocol 5: Statistical analysis of the data.
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Affiliation(s)
- Arjun Sengupta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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33
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Capuccini M, Larsson A, Carone M, Novella JA, Sadawi N, Gao J, Toor S, Spjuth O. On-demand virtual research environments using microservices. PeerJ Comput Sci 2019; 5:e232. [PMID: 33816885 PMCID: PMC7924445 DOI: 10.7717/peerj-cs.232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/10/2019] [Indexed: 06/12/2023]
Abstract
The computational demands for scientific applications are continuously increasing. The emergence of cloud computing has enabled on-demand resource allocation. However, relying solely on infrastructure as a service does not achieve the degree of flexibility required by the scientific community. Here we present a microservice-oriented methodology, where scientific applications run in a distributed orchestration platform as software containers, referred to as on-demand, virtual research environments. The methodology is vendor agnostic and we provide an open source implementation that supports the major cloud providers, offering scalable management of scientific pipelines. We demonstrate applicability and scalability of our methodology in life science applications, but the methodology is general and can be applied to other scientific domains.
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Affiliation(s)
- Marco Capuccini
- Department of Information Technology, Uppsala University, Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Anders Larsson
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Matteo Carone
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Jon Ander Novella
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Noureddin Sadawi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Jianliang Gao
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Salman Toor
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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34
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Cardoso S, Afonso T, Maraschin M, Rocha M. WebSpecmine: A Website for Metabolomics Data Analysis and Mining. Metabolites 2019; 9:metabo9100237. [PMID: 31635085 PMCID: PMC6835413 DOI: 10.3390/metabo9100237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022] Open
Abstract
Metabolomics data analysis is an important task in biomedical research. The available tools do not provide a wide variety of methods and data types, nor ways to store and share data and results generated. Thus, we have developed WebSpecmine to overcome the aforementioned limitations. WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS) and compound concentrations. Users, even those not possessing programming skills, can access several analysis methods including univariate, unsupervised and supervised multivariate statistical analysis, as well as metabolite identification and pathway analysis, also being able to create accounts to store their data and results, either privately or publicly. The tool's implementation is based in the R project, including its shiny web-based framework. Webspecmine is freely available, supporting all major browsers. We provide abundant documentation, including tutorials and a user guide with case studies.
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Affiliation(s)
- Sara Cardoso
- CEB-Centre Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
| | - Telma Afonso
- CEB-Centre Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
| | - Marcelo Maraschin
- Plant Morphogenesis and Biochemistry Laboratory, Federal University of Santa Catarina, Florianópolis SC 88040-900, Brazil.
| | - Miguel Rocha
- CEB-Centre Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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35
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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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36
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Khalili B, Tomasoni M, Mattei M, Mallol Parera R, Sonmez R, Krefl D, Rueedi R, Bergmann S. Automated Analysis of Large-Scale NMR Data Generates Metabolomic Signatures and Links Them to Candidate Metabolites. J Proteome Res 2019; 18:3360-3368. [PMID: 31318216 DOI: 10.1021/acs.jproteome.9b00295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of metabolites in large-scale 1H NMR data from human biofluids remains challenging due to the complexity of the spectra and their sensitivity to pH and ionic concentrations. In this work, we tested the capacity of three analysis tools to extract metabolite signatures from 968 NMR profiles of human urine samples. Specifically, we studied sets of covarying features derived from principal component analysis (PCA), the iterative signature algorithm (ISA), and averaged correlation profiles (ACP), a new method we devised inspired by the STOCSY approach. We used our previously developed metabomatching method to match the sets generated by these algorithms to NMR spectra of individual metabolites available in public databases. On the basis of the number and quality of the matches, we concluded that ISA and ACP can robustly identify ten and nine metabolites, respectively, half of which were shared, while PCA did not produce any signatures with robust matches.
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Affiliation(s)
- Bita Khalili
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Mattia Tomasoni
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Mirjam Mattei
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Roger Mallol Parera
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Reyhan Sonmez
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Daniel Krefl
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Rico Rueedi
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Sven Bergmann
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland.,Department of Integrative Biomedical Sciences , University of Cape Town , Cape Town 7700 , South Africa
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Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS. NMR Spectroscopy for Metabolomics Research. Metabolites 2019; 9:E123. [PMID: 31252628 PMCID: PMC6680826 DOI: 10.3390/metabo9070123] [Citation(s) in RCA: 481] [Impact Index Per Article: 96.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, Formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Uttar Pradesh 226014, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA
| | - Fatimah Alahmari
- Department of NanoMedicine Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia
| | - Lukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
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38
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Williams CM, Rocca JR, Edison AS, Allison DB, Morgan TJ, Hahn DA. Cold adaptation does not alter ATP homeostasis during cold exposure in Drosophila melanogaster. Integr Zool 2019; 13:471-481. [PMID: 29722155 DOI: 10.1111/1749-4877.12326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In insects and other ectotherms, cold temperatures cause a coma resulting from loss of neuromuscular function, during which ionic and metabolic homeostasis are progressively lost. Cold adaptation improves homeostasis during cold exposure, but the ultimate targets of selection are still an open question. Cold acclimation and adaptation remodels mitochondrial metabolism in insects, suggesting that aerobic energy production during cold exposure could be a target of selection. Here, we test the hypothesis that cold adaptation improves the ability to maintain rates of aerobic energy production during cold exposure by using 31 P NMR on live flies. Using lines of Drosophila melanogaster artificially selected for fast and slow recovery from a cold coma, we show that cold exposure does not lower ATP levels and that cold adaptation does not alter aerobic ATP production during cold exposure. Cold-hardy and cold-susceptible lines both experienced a brief transition to anaerobic metabolism during cooling, but this was rapidly reversed during cold exposure, suggesting that oxidative phosphorylation was sufficient to meet energy demands below the critical thermal minimum, even in cold-susceptible flies. We thus reject the hypothesis that performance under mild low temperatures is set by aerobic ATP supply limitations in D. melanogaster, excluding oxygen and capacity limitation as a weak link in energy supply. This work suggests that the modulations to mitochondrial metabolism resulting from cold acclimation or adaptation may arise from selection on a biosynthetic product(s) of those pathways rather than selection on ATP supply during cold exposure.
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Affiliation(s)
- Caroline M Williams
- Department of Integrative Biology, University of California, Berkeley, California, USA.,Departments of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - James R Rocca
- Advanced Magnetic Resonance Imaging and Spectroscopy Facility, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Arthur S Edison
- Departments of Entomology and Biochemistry, University of Florida, Gainesville, Florida, USA.,Departments of Genetics and Biochemistry, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - David B Allison
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Theodore J Morgan
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Daniel A Hahn
- Departments of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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39
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Paudel L, Nagana Gowda GA, Raftery D. Extractive Ratio Analysis NMR Spectroscopy for Metabolite Identification in Complex Biological Mixtures. Anal Chem 2019; 91:7373-7378. [PMID: 31059230 DOI: 10.1021/acs.analchem.9b01235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The complexity of biological mixtures continues to challenge efforts aimed at unknown metabolite identification in the metabolomics field. To address this challenge, we provide a new method to identify related peaks from individual metabolites in complex NMR spectra. Extractive ratio analysis NMR spectroscopy (E-RANSY) builds on our previously described ratio analysis method [ Wei et al. Anal. Chem. 2011 , 83 , 7616 - 7623 ] and exploits the simplified NMR spectra provided by the extraction of metabolites under varied pH conditions. Under such conditions, metabolites from the same biological specimen are extracted differentially, and the resulting NMR spectra exhibit characteristics favorable for unraveling unknown metabolite peaks using ratio analysis. We demonstrate the utility of the E-RANSY method by extracting carboxylic acid containing metabolites from human urine, one of the highly complex biological mixtures encountered in the metabolomics field. E-RANSY performs better than STOCSY and the original RANSY method and offers new avenues to identify unknown metabolites in complex biological mixtures.
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Affiliation(s)
| | | | - Daniel Raftery
- Fred Hutchinson Cancer Research Center , Seattle , Washington 98109 , United States
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40
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Matviychuk Y, Yeo J, Holland DJ. A field-invariant method for quantitative analysis with benchtop NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 298:35-47. [PMID: 30529048 DOI: 10.1016/j.jmr.2018.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Recently developed benchtop instruments have the potential of bringing the benefits of NMR spectroscopy to the wide variety of industrial applications. Unfortunately, their low spectral resolution poses significant challenges for traditional quantification approach. Here we present a novel model-based method designed to overcome these challenges. By defining our models in terms of quantum mechanical properties of the underlying spin system, we make our approach invariant to the spectrometer field strength and especially suitable for analyzing benchtop data. Our experimental results on prepared samples and natural fruit juices confirm the applicability of our method for quantitative analysis of medium-field 1H NMR spectra. The developed method succeeds in accurately separating the spectra of glucose anomers and even monitoring their interconversion in non-deuterated water. Furthermore, the compositions of unbuffered natural fruit juices estimated using data from 43 MHz to 400 MHz spectrometers are in good agreement with each other and with the reference values from nutrition databases.
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Affiliation(s)
- Yevgen Matviychuk
- University of Canterbury, Private Bag 4800, Cristchurch 8140, New Zealand
| | - Jet Yeo
- University of Canterbury, Private Bag 4800, Cristchurch 8140, New Zealand
| | - Daniel J Holland
- University of Canterbury, Private Bag 4800, Cristchurch 8140, New Zealand.
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41
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Abstract
NMR spectroscopy is one of the major analytical techniques used in the metabolomics studies of food. There are many applications of metabolomics on food-related topics and on the food itself. Here, we describe protocols for performing NMR-based metabolomics of foods ranging from simple beverages to solid foods and semisolid foods. Beverages can be analyzed either directly or after sample preprocessing to remove interfering macromolecules, muscle-based foods can be analyzed after extraction, and semisolid foods can be analyzed directly using high-resolution magic-angle spinning (HR-MAS) NMR. Finally, we discuss metabolomic data analysis as well as different procedures and strategies for targeted and untargeted approaches.
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Affiliation(s)
| | - Nina Eggers
- Department of Food Science, Aarhus University, Årslev, Denmark
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42
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Sokolenko S, Jézéquel T, Hajjar G, Farjon J, Akoka S, Giraudeau P. Robust 1D NMR lineshape fitting using real and imaginary data in the frequency domain. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 298:91-100. [PMID: 30530098 DOI: 10.1016/j.jmr.2018.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Quantitative NMR is intrinsically dependent on precise, accurate, and robust peak area calculation. In this work, we demonstrate how the use of complex-valued peak descriptions can improve peak fitting in the frequency domain - incorporating phase and baseline correction as well as apodization while working with commonly used Fourier-transformed data. The method has been implemented in an open source R package called rnmrfit that is available for download on GitHub (https://github.com/ssokolen/rnmrfit). Application to real data suggests that this approach can also result in dramatically higher precision than can be achieved with existing software. Simulation data indicates that coefficients of variation below 0.1% can be readily achieved at signal to noise (SNR) ratios of approximately 100. The use of complex-valued data in the frequency domain is demonstrated as a relatively simple and effective means of improving peak fitting for quantitative NMR analysis.
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Affiliation(s)
- Stanislav Sokolenko
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington St., PO Box 15000, Halifax, NS B3H 4R2, Canada.
| | - Tangi Jézéquel
- CEISAM, UMR CNRS 6230, Bât. 22 Faculté des Sciences et Techniques 2 rue de la Houssinière, 44322 Nantes Cedex 03, France
| | - Ghina Hajjar
- CEISAM, UMR CNRS 6230, Bât. 22 Faculté des Sciences et Techniques 2 rue de la Houssinière, 44322 Nantes Cedex 03, France; Laboratory of Metrology and Isotopic Fractionation, Research Unit: Technologies et Valorisation Agroalimentaire (TVA), Faculty of Science, Saint-Joseph University of Beirut, PO Box 17-5208 Mar Mikhael, Beirut 1104 2020, Lebanon
| | - Jonathan Farjon
- CEISAM, UMR CNRS 6230, Bât. 22 Faculté des Sciences et Techniques 2 rue de la Houssinière, 44322 Nantes Cedex 03, France
| | - Serge Akoka
- CEISAM, UMR CNRS 6230, Bât. 22 Faculté des Sciences et Techniques 2 rue de la Houssinière, 44322 Nantes Cedex 03, France
| | - Patrick Giraudeau
- CEISAM, UMR CNRS 6230, Bât. 22 Faculté des Sciences et Techniques 2 rue de la Houssinière, 44322 Nantes Cedex 03, France; Institut Universitaire de France, 1 rue Descartes, 75005 Paris Cedex 05, France
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43
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Abstract
NMR data from large studies combining multiple cohorts is becoming common in large-scale metabolomics. The data size and combination of cohorts with diverse properties leads to special problems for data processing and analysis. These include alignment, normalization, detection and removal of outliers, presence of strong correlations, and the identification of unknowns. Nonetheless, these challenges can be addressed with suitable algorithms and techniques, leading to enhanced data sets ripe for further data mining.
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44
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Asakura T, Date Y, Kikuchi J. Application of ensemble deep neural network to metabolomics studies. Anal Chim Acta 2018; 1037:230-236. [DOI: 10.1016/j.aca.2018.02.045] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 02/05/2018] [Accepted: 02/10/2018] [Indexed: 10/18/2022]
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45
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Puig-Castellví F, Pérez Y, Piña B, Tauler R, Alfonso I. Comparative analysis of 1H NMR and 1H- 13C HSQC NMR metabolomics to understand the effects of medium composition in yeast growth. Anal Chem 2018; 90:12422-12430. [PMID: 30350620 DOI: 10.1021/acs.analchem.8b01196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In nuclear magnetic resonance (NMR) metabolomics, most of the studies have been focused on the analysis of one-dimensional proton (1D 1H) NMR, whereas the analysis of other nuclei, such as 13C, or other NMR experiments are still underrepresented. The preference of 1D 1H NMR metabolomics lies on the fact that it has good sensitivity and a short acquisition time, but it lacks spectral resolution because it presents a high degree of overlap. In this study, the growth metabolism of yeast ( Saccharomyces cerevisiae) was analyzed by 1D 1H NMR and by two-dimensional (2D) 1H-13C heteronuclear single quantum coherence (HSQC) NMR spectroscopy, leading to the detection of more than 50 metabolites with both analytical approaches. These two analyses allow for a better understanding of the strengths and intrinsic limitations of the two types of NMR approaches. The two data sets (1D and 2D NMR) were investigated with PCA, ASCA, and PLS DA chemometric methods, and similar results were obtained regardless of the data type used. However, data-analysis time for the 2D NMR data set was substantially reduced when compared with the data analysis of the corresponding 1H NMR data set because, for the 2D NMR data, signal overlap was not a major problem and deconvolution was not required. The comparative study described in this work can be useful for the future design of metabolomics workflows, to assist in the selection of the most convenient NMR platform and to guide the posterior data analysis of biomarker selection.
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Affiliation(s)
- Francesc Puig-Castellví
- Department of Environmental Chemistry , Institute of Environmental Assessment and Water Research (IDAEA-CSIC) , Jordi Girona 18-26 , 08034 Barcelona , Spain
| | - Yolanda Pérez
- NMR Facility , Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , 08034 Barcelona , Spain
| | - Benjamín Piña
- Department of Environmental Chemistry , Institute of Environmental Assessment and Water Research (IDAEA-CSIC) , Jordi Girona 18-26 , 08034 Barcelona , Spain
| | - Romà Tauler
- Department of Environmental Chemistry , Institute of Environmental Assessment and Water Research (IDAEA-CSIC) , Jordi Girona 18-26 , 08034 Barcelona , Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry , Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , 08034 Barcelona , Spain
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46
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Cañueto D, Salek RM, Correig X, Cañellas N. Improving sample classification by harnessing the potential of 1H-NMR signal chemical shifts. Sci Rep 2018; 8:11886. [PMID: 30089873 PMCID: PMC6082897 DOI: 10.1038/s41598-018-30351-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
NMR spectroscopy is a technology that is widely used in metabolomic studies. The information that these studies most commonly use from NMR spectra is the metabolite concentration. However, as well as concentration, pH and ionic strength information are also made available by the chemical shift of metabolite signals. This information is typically not used even though it can enhance sample discrimination, since many conditions show pH or ionic imbalance. Here, we demonstrate how chemical shift information can be used to improve the quality of the discrimination between case and control samples in three public datasets of different human matrices. In two of these datasets, chemical shift information helped to provide an AUROC value higher than 0.9 during sample classification. In the other dataset, the chemical shift also showed discriminant potential (AUROC 0.831). These results are consistent with the pH imbalance characteristic of the condition studied in the datasets. In addition, we show that this signal misalignment dependent on sample class can alter the results of fingerprinting approaches in the three datasets. Our results show that it is possible to use chemical shift information to enhance the diagnostic and predictive properties of NMR.
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Affiliation(s)
- Daniel Cañueto
- Metabolomics Platform, IISPV, DEEEA, Universitat Rovira i Virgili, Campus Sescelades, Carretera de Valls, s/n, 43007, Tarragona, Catalonia, Spain.
| | - Reza M Salek
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Xavier Correig
- Metabolomics Platform, IISPV, DEEEA, Universitat Rovira i Virgili, Campus Sescelades, Carretera de Valls, s/n, 43007, Tarragona, Catalonia, Spain
- CIBERDEM, Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders, Madrid, Spain
| | - Nicolau Cañellas
- Metabolomics Platform, IISPV, DEEEA, Universitat Rovira i Virgili, Campus Sescelades, Carretera de Valls, s/n, 43007, Tarragona, Catalonia, Spain.
- CIBERDEM, Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders, Madrid, Spain.
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47
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Verhoeven A, Giera M, Mayboroda OA. KIMBLE: A versatile visual NMR metabolomics workbench in KNIME. Anal Chim Acta 2018; 1044:66-76. [PMID: 30442406 DOI: 10.1016/j.aca.2018.07.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 01/17/2023]
Abstract
The problem of reproducibility of scientific research is a serious issue in biomedical sciences. In addition to experimental repeatability, limiting the (pre-) analytical variance is also essential. To address this problem in the field of metabolomics, we have designed KIMBLE, the KNIME-based Integrated MetaBoLomics Environment, a novel platform for the processing and analysis of NMR metabolomics data. It consists of an elaborate NMR metabolomics workflow in the KNIME workflow management system that handles both targeted and untargeted metabolomics. The workflow provides a self-documenting way of transforming raw time-domain NMR data into metabolic insights. Parameters for the quantification of a number of interesting metabolites in urine are included in the workflow, and several useful statistical analysis and visualization tools are incorporated as well. The workflow comes with an interesting sports-induced ketosis dataset so that new users can easily get acquainted with the platform. The user is free to adapt and extend the workflow to his or her personal needs. The KIMBLE workflow, the KNIME software and all the required libraries are installed in a VirtualBox virtual machine that allows for facile installation and use by non-experts.
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Affiliation(s)
- Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands.
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
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Puig-Castellví F, Bedia C, Alfonso I, Piña B, Tauler R. Deciphering the Underlying Metabolomic and Lipidomic Patterns Linked to Thermal Acclimation in Saccharomyces cerevisiae. J Proteome Res 2018; 17:2034-2044. [PMID: 29707950 DOI: 10.1021/acs.jproteome.7b00921] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Temperature is one of the most critical parameters for yeast growth, and it has deep consequences in many industrial processes where yeast is involved. Nevertheless, the metabolic changes required to accommodate yeast cells at high or low temperatures are still poorly understood. In this work, the ultimate responses of these induced transcriptomic effects have been examined using metabolomics-derived strategies. The yeast metabolome and lipidome have been characterized by 1D proton nuclear magnetic resonance spectroscopy and ultra-high-performance liquid chromatography-mass spectrometry at four temperatures, corresponding to low, optimal, high, and extreme thermal conditions. The underlying pathways that drive the acclimation response of yeast to these nonoptimal temperatures were evaluated using multivariate curve resolution-alternating least-squares. The analysis revealed three different thermal profiles (cold, optimal, and high temperature), which include changes in the lipid composition, secondary metabolic pathways, and energy metabolism, and we propose that they reflect the acclimation strategy of yeast cells to low and high temperatures. The data suggest that yeast adjusts membrane fluidity by changing the relative proportions of the different lipid families (acylglycerides, phospholipids, and ceramides, among others) rather than modifying the average length and unsaturation levels of the corresponding fatty acids.
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Affiliation(s)
- Francesc Puig-Castellví
- Department of Environmental Chemistry , IDAEA-CSIC , Jordi Girona 18-26 , Barcelona 08034 , Catalonia , Spain
| | - Carmen Bedia
- Department of Environmental Chemistry , IDAEA-CSIC , Jordi Girona 18-26 , Barcelona 08034 , Catalonia , Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling , IQAC-CSIC , Jordi Girona 18-26 , Barcelona 08034 , Catalonia , Spain
| | - Benjamin Piña
- Department of Environmental Chemistry , IDAEA-CSIC , Jordi Girona 18-26 , Barcelona 08034 , Catalonia , Spain
| | - Romà Tauler
- Department of Environmental Chemistry , IDAEA-CSIC , Jordi Girona 18-26 , Barcelona 08034 , Catalonia , Spain
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Abstract
Abstract
Next Generation Sequencing (NGS) or deep sequencing technology enables parallel reading of multiple individual DNA fragments, thereby enabling the identification of millions of base pairs in several hours. Recent research has clearly shown that machine learning technologies can efficiently analyse large sets of genomic data and help to identify novel gene functions and regulation regions. A deep artificial neural network consists of a group of artificial neurons that mimic the properties of living neurons. These mathematical models, termed Artificial Neural Networks (ANN), can be used to solve artificial intelligence engineering problems in several different technological fields (e.g., biology, genomics, proteomics, and metabolomics). In practical terms, neural networks are non-linear statistical structures that are organized as modelling tools and are used to simulate complex genomic relationships between inputs and outputs. To date, Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNN) have been demonstrated to be the best tools for improving performance in problem solving tasks within the genomic field.
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50
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Beirnaert C, Meysman P, Vu TN, Hermans N, Apers S, Pieters L, Covaci A, Laukens K. speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification. PLoS Comput Biol 2018; 14:e1006018. [PMID: 29494588 PMCID: PMC5849334 DOI: 10.1371/journal.pcbi.1006018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 03/13/2018] [Accepted: 02/04/2018] [Indexed: 01/18/2023] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq).
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Affiliation(s)
- Charlie Beirnaert
- Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
- * E-mail: (CB); (KL)
| | - Pieter Meysman
- Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nina Hermans
- Natural Products & Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Sandra Apers
- Natural Products & Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Luc Pieters
- Natural Products & Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Adrian Covaci
- Toxicological Center, Department of Pharmaceutical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
- * E-mail: (CB); (KL)
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