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Höcker O, Flottmann D, Schmidt TC, Neusüß C. Non-targeted LC-MS and CE-MS for biomarker discovery in bioreactors: Influence of separation, mass spectrometry and data processing tools. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149012. [PMID: 34325133 DOI: 10.1016/j.scitotenv.2021.149012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Liquid separation coupled to mass spectrometry is often used for non-targeted analyses in various fields, such as metabolomics. However, the combination of non-standardized methods, various mass spectrometers (MS) and processing tools for data evaluation affect biomarker discovery potentially. Here, we present a comprehensive study of these factors based on non-targeted liquid chromatography coupled to time-of-flight (TOF) and Orbitrap MS and capillary zone electrophoresis to Orbitrap analyses of the same bioreactor samples, describing the correlation of its gas yield with changing feature signal intensity. The three datasets were processed with MZmine 2 and XCMS online and subsequential Partial Least Square Regression (PLSR) with Variable Importance in Projection (VIP) ranking for feature prioritization. The six feature tables were compared to evaluate their overlap of shared features and the influence of the processing software and MS instrument on the VIP values and fold changes. The overlaps, defined as a fraction of one feature table found in the comparative table, were from 27% to 57% for the comparison of MZmine and XCMS and from 15% to 50% between Orbitrap and TOF data sets, respectively. Considering the most relevant features only (VIP >1.5), the overlaps were increased significantly in all cases from 26% to 95%. For the same data set, both VIP values and fold changes were well correlated, however, varied significantly between TOF and Orbitrap. CE-MS showed higher total feature numbers compared to LC-MS, most likely due to its more appropriate selectivity, different sample preparation, and/or the sensitive nano-ESI interface. Since only less than 10% of MS/MS data overlapped, CE-MS provided complementary information to LC-MS. Overall, our systematic study proves the benefits of using different separation techniques and processing tools but also indicates a significant influence of mass spectrometry on comprehensive biomarker discovery.
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Affiliation(s)
- Oliver Höcker
- Department of Chemistry, Aalen University, D-73430 Aalen, Germany; Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, D-45141 Essen, Germany
| | - Dirk Flottmann
- Department of Chemistry, Aalen University, D-73430 Aalen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, D-45141 Essen, Germany
| | - Christian Neusüß
- Department of Chemistry, Aalen University, D-73430 Aalen, Germany.
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2
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Mamani-Huanca M, de la Fuente AG, Otero A, Gradillas A, Godzien J, Barbas C, López-Gonzálvez Á. Enhancing confidence of metabolite annotation in Capillary Electrophoresis-Mass Spectrometry untargeted metabolomics with relative migration time and in-source fragmentation. J Chromatogr A 2020; 1635:461758. [PMID: 33302137 DOI: 10.1016/j.chroma.2020.461758] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
Capillary electrophoresis coupled to mass spectrometry is a power tool in untargeted metabolomics studies to analyze charged and polar compounds. However, identification is a challenge due to the variability of migration times and the lack of MS/MS spectra in CE-TOF-MS, the type of instruments most frequently employed. We present here a CE-MS search platform incorporated in CEU Mass Mediator to annotate metabolites with a confidence level L2. For its the development we analyzed 226 compounds using two fragmentor voltages: 100 and 200 V. The information obtained, such as relative migration times (RMT) and in-source fragments, were incorporated into the platform. In addition, we validated the CE-MS search functionality using different types of biological samples such as plasma samples (human, rat, and rabbit), mouse macrophages, and human urine. The RMT tolerance percentage for the search of metabolites has been determined, establishing 5% for all compounds, except for the compounds migrating in the electro-osmotic flow, for which the tolerance should be of 10%. It has also been demonstrated the robustness of the in-source fragmentation, which makes possible the annotation of compounds by means of their fragmentation pattern. As an example, 3-methylhistidine and 1-methilhistidine, whose RMT are very close, have been annotated. Studies of the fragmentation mechanisms of acyl-L-carnitines have shown that in-source fragmentation follows the general fragmentation rules and is a suitable alternative to MS/MS.
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Affiliation(s)
- Maricruz Mamani-Huanca
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Alberto Gil de la Fuente
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Department of Information Technology, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Abraham Otero
- Department of Information Technology, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
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Sailwal M, Das AJ, Gazara RK, Dasgupta D, Bhaskar T, Hazra S, Ghosh D. Connecting the dots: Advances in modern metabolomics and its application in yeast system. Biotechnol Adv 2020; 44:107616. [DOI: 10.1016/j.biotechadv.2020.107616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022]
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4
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Identification of antihypertensive peptides in nutraceuticals by capillary electrophoresis-mass spectrometry. J Chromatogr A 2018; 1579:129-137. [DOI: 10.1016/j.chroma.2018.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/28/2018] [Accepted: 10/13/2018] [Indexed: 01/30/2023]
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5
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Metabolomics in chronic kidney disease: Strategies for extended metabolome coverage. J Pharm Biomed Anal 2018; 161:313-325. [PMID: 30195171 DOI: 10.1016/j.jpba.2018.08.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/16/2022]
Abstract
Chronic kidney disease (CKD) is becoming a major public health issue as prevalence is increasing worldwide. It also represents a major challenge for the identification of new early biomarkers, understanding of biochemical mechanisms, patient monitoring and prognosis. Each metabolite contained in a biofluid or tissue may play a role as a signal or as a driver in the development or progression of the pathology. Therefore, metabolomics is a highly valuable approach in this clinical context. It aims to provide a representative picture of a biological system, making exhaustive metabolite coverage crucial. Two aspects can be considered: analytical and biological coverage. From an analytical point of view, monitoring all metabolites within one run is currently impossible. Multiple analytical techniques providing orthogonal information should be carried out in parallel for coverage improvement. The biological aspect of metabolome coverage can be enhanced by using multiple biofluids or tissues for in-depth biological investigation, as the analysis of a single sample type is generally insufficient for whole organism extrapolation. Hence, recording of signals from multiple sample types and different analytical platforms generates massive and complex datasets so that chemometric tools, including data fusion approaches and multi-block analysis, are key tools for extracting biological information and for discovery of relevant biomarkers. This review presents the recent developments in the field of metabolomic analysis, from sampling and analytical strategies to chemometric tools, dedicated to the generation and handling of multiple complementary metabolomic datasets enabling extended metabolite coverage to improve our biological knowledge of CKD.
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Navarro-Reig M, Jaumot J, Piña B, Moyano E, Galceran MT, Tauler R. Metabolomic analysis of the effects of cadmium and copper treatment in Oryza sativa L. using untargeted liquid chromatography coupled to high resolution mass spectrometry and all-ion fragmentation. Metallomics 2018; 9:660-675. [PMID: 28480907 DOI: 10.1039/c6mt00279j] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
While the knowledge of plant metabolomes has increased in the last few years, their response to the presence of toxicants is still poorly understood. Here, we analyse the metabolomic changes in Japanese rice (Oryza sativa var. Japonica) upon exposure to heavy metals (Cd(ii) and Cu(ii)) in concentrations from 10 to 1000 μM. After harvesting, rice metabolites were extracted from aerial parts of the plants and analysed by HPLC (HILIC TSK gel amide-80 column) coupled to a mass spectrometer quadrupole-Orbitrap (Q-Exactive). Full scan and all ion fragmentation (AIF) mass spectrometry modes were used during the analysis. The proposed untargeted metabolomics data analysis strategy is based on the application of the multivariate curve resolution alternating least squares (MCR-ALS) method for feature detection, allowing the simultaneous resolution of pure chromatographic profiles and mass spectra of all metabolites present in the analysed rice extracts. All-ion fragmentation data were used to confirm the identification of MCR-ALS resolved metabolites. A total of 112 metabolites were detected, and 97 of them were subsequently identified and confirmed. Pathway analysis of the observed metabolic changes suggested an underlying similarity of the responses of the plant to Cd(ii) and Cu(ii), although the former treatment appeared to be the more severe of the two. In both cases, secondary metabolism and amino acid-, purine-, carbon- and glycerolipid-metabolism pathways were affected, in a pattern consistent with reduction in plant growth and/or photosynthetic capacity and with induction of defence mechanisms to reduce cell damage.
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Affiliation(s)
- Meritxell Navarro-Reig
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
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7
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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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8
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A chemometric approach for characterization of serum transthyretin in familial amyloidotic polyneuropathy type I (FAP-I) by electrospray ionization-ion mobility mass spectrometry. Talanta 2018; 181:87-94. [DOI: 10.1016/j.talanta.2017.12.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 01/19/2023]
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9
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González-Ruiz V, Gagnebin Y, Drouin N, Codesido S, Rudaz S, Schappler J. ROMANCE: A new software tool to improve data robustness and feature identification in CE-MS metabolomics. Electrophoresis 2018; 39:1222-1232. [DOI: 10.1002/elps.201700427] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/14/2017] [Accepted: 12/14/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Víctor González-Ruiz
- School of Pharmaceutical Sciences; University of Geneva; University of Lausanne; Geneva Switzerland
| | - Yoric Gagnebin
- School of Pharmaceutical Sciences; University of Geneva; University of Lausanne; Geneva Switzerland
| | - Nicolas Drouin
- School of Pharmaceutical Sciences; University of Geneva; University of Lausanne; Geneva Switzerland
| | | | - Serge Rudaz
- School of Pharmaceutical Sciences; University of Geneva; University of Lausanne; Geneva Switzerland
| | - Julie Schappler
- School of Pharmaceutical Sciences; University of Geneva; University of Lausanne; Geneva Switzerland
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10
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Ortiz-Villanueva E, Navarro-Martín L, Jaumot J, Benavente F, Sanz-Nebot V, Piña B, Tauler R. Metabolic disruption of zebrafish (Danio rerio) embryos by bisphenol A. An integrated metabolomic and transcriptomic approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:22-36. [PMID: 28780062 DOI: 10.1016/j.envpol.2017.07.095] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 06/07/2023]
Abstract
Although bisphenol A (BPA) is commonly recognized as an endocrine disruptor, the metabolic consequences of its exposure are still poorly understood. In this study, we present a non-targeted LC-MS based metabolomic analysis in combination with a full-genome, high-throughput RNA sequencing (RNA-Seq) to reveal the metabolic effects and the subjacent regulatory pathways of exposing zebrafish embryos to BPA during the first 120 hours post-fertilization. We applied multivariate data analysis methods to extract biochemical information from the LC-MS and RNA-Seq complex datasets and to perform testable predictions of the phenotypic adverse effects. Metabolomic and transcriptomic data revealed a similar subset of altered pathways, despite the large difference in the number of identified biomarkers (around 50 metabolites and more than 1000 genes). These results suggest that even a moderate coverage of zebrafish metabolome may be representative of the global metabolic changes. These multi-omic responses indicate a specific metabolic disruption by BPA affecting different signaling pathways, such as retinoid and prostaglandin metabolism. The combination of transcriptomic and metabolomic data allowed a dynamic interpretation of the results that could not be drawn from either single dataset. These results illustrate the utility of -omic integrative analyses for characterizing the physiological effects of toxicants beyond the mere indication of the affected pathways.
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Affiliation(s)
- Elena Ortiz-Villanueva
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Laia Navarro-Martín
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Joaquim Jaumot
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Benjamín Piña
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
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11
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Ortiz-Villanueva E, Benavente F, Piña B, Sanz-Nebot V, Tauler R, Jaumot J. Knowledge integration strategies for untargeted metabolomics based on MCR-ALS analysis of CE-MS and LC-MS data. Anal Chim Acta 2017; 978:10-23. [DOI: 10.1016/j.aca.2017.04.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 03/07/2017] [Accepted: 04/25/2017] [Indexed: 12/15/2022]
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12
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Puig-Castellví F, Alfonso I, Tauler R. Untargeted assignment and automatic integration of 1H NMR metabolomic datasets using a multivariate curve resolution approach. Anal Chim Acta 2017; 964:55-66. [PMID: 28351639 DOI: 10.1016/j.aca.2017.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 01/06/2023]
Abstract
In this article, we propose the use of the Multivariate Curve Resolution - Alternating Least Squares (MCR-ALS) chemometrics method to resolve the 1H NMR spectra and concentration of the individual metabolites in their mixtures in untargeted metabolomics studies. A decision tree-based strategy is presented to optimally select and implement spectra estimates and equality constraints during MCR-ALS optimization. The proposed method has been satisfactorily evaluated using different 1H NMR metabolomics datasets. In a first study, 1H NMR spectra of the metabolites in a simulated mixture were successfully recovered and assigned. In a second study, more than 30 metabolites were characterized and quantified from an experimental unknown mixture analyzed by 1H NMR. In this work, MCR-ALS is shown to be a convenient tool for metabolite investigation and sample screening using 1H NMR, and it opens a new path for performing metabolomics studies with this chemometric technique.
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Affiliation(s)
- Francesc Puig-Castellví
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain.
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13
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Gorrochategui E, Li J, Fullwood NJ, Ying GG, Tian M, Cui L, Shen H, Lacorte S, Tauler R, Martin FL. Diet-sourced carbon-based nanoparticles induce lipid alterations in tissues of zebrafish (Danio rerio) with genomic hypermethylation changes in brain. Mutagenesis 2016; 32:91-103. [PMID: 27798195 PMCID: PMC5180172 DOI: 10.1093/mutage/gew050] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
With rising environmental levels of carbon-based nanoparticles (CBNs), there is an urgent need to develop an understanding of their biological effects in order to generate appropriate risk assessment strategies. Herein, we exposed zebrafish via their diet to one of four different CBNs: C60 fullerene (C60), single-walled carbon nanotubes (SWCNT), short multi-walled carbon nanotubes (MWCNTs) or long MWCNTs. Lipid alterations in male and female zebrafish were explored post-exposure in three target tissues (brain, gonads and gastrointestinal tract) using ‘omic’ procedures based in liquid chromatography coupled with mass spectrometry (LC-MS) data files. These tissues were chosen as they are often target tissues following environmental exposure. Marked alterations in lipid species are noted in all three tissues. To further explore CBN-induced brain alterations, Raman microspectroscopy analysis of lipid extracts was conducted. Marked lipid alterations are observed with males responding differently to females; in addition, there also appears to be consistent elevations in global genomic methylation. This latter observation is most profound in female zebrafish brain tissues post-exposure to short MWCNTs or SWCNTs (P < 0.05). This study demonstrates that even at low levels, CBNs are capable of inducing significant cellular and genomic modifications in a range of tissues. Such alterations could result in modified susceptibility to other influences such as environmental exposures, pathology and, in the case of brain, developmental alterations.
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Affiliation(s)
- Eva Gorrochategui
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08034, Catalonia, Spain
| | | | - Nigel J Fullwood
- Biomedical and Life Sciences Division, Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Guang-Guo Ying
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Meiping Tian
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China and
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China and
| | - Heqing Shen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China and
| | - Sílvia Lacorte
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08034, Catalonia, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08034, Catalonia, Spain
| | - Francis L Martin
- Centre for Biophotonics and .,Biosciences, School of Pharmacy and Biomedical Sciences, Maudland Building, University of Central Lancashire, Preston PR1 2HE, UK
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Týčová A, Ledvina V, Klepárník K. Recent advances in CE-MS coupling: Instrumentation, methodology, and applications. Electrophoresis 2016; 38:115-134. [DOI: 10.1002/elps.201600366] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Týčová
- Institute of Analytical Chemistry; Czech Academy of Sciences; Brno Czech Republic
| | - Vojtěch Ledvina
- Institute of Analytical Chemistry; Czech Academy of Sciences; Brno Czech Republic
| | - Karel Klepárník
- Institute of Analytical Chemistry; Czech Academy of Sciences; Brno Czech Republic
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15
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Gorrochategui E, Jaumot J, Lacorte S, Tauler R. Data analysis strategies for targeted and untargeted LC-MS metabolomic studies: Overview and workflow. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.07.004] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Puig-Castellví F, Alfonso I, Piña B, Tauler R. (1)H NMR metabolomic study of auxotrophic starvation in yeast using Multivariate Curve Resolution-Alternating Least Squares for Pathway Analysis. Sci Rep 2016; 6:30982. [PMID: 27485935 PMCID: PMC4971537 DOI: 10.1038/srep30982] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/12/2016] [Indexed: 11/15/2022] Open
Abstract
Disruption of specific metabolic pathways constitutes the mode of action of many known toxicants and it is responsible for the adverse phenotypes associated to human genetic defects. Conversely, many industrial applications rely on metabolic alterations of diverse microorganisms, whereas many therapeutic drugs aim to selectively disrupt pathogens’ metabolism. In this work we analyzed metabolic changes induced by auxotrophic starvation conditions in yeast in a non-targeted approach, using one-dimensional proton Nuclear Magnetic Resonance spectroscopy (1H NMR) and chemometric analyses. Analysis of the raw spectral datasets showed specific changes linked to the different stages during unrestricted yeast growth, as well as specific changes linked to each of the four tested starvation conditions (L-methionine, L-histidine, L-leucine and uracil). Analysis of changes in concentrations of more than 40 metabolites by Multivariate Curve Resolution – Alternating Least Squares (MCR-ALS) showed the normal progression of key metabolites during lag, exponential and stationary unrestricted growth phases, while reflecting the metabolic blockage induced by the starvation conditions. In this case, different metabolic intermediates accumulated over time, allowing identification of the different metabolic pathways specifically affected by each gene disruption. This synergy between NMR metabolomics and molecular biology may have clear implications for both genetic diagnostics and drug development.
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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, Catalonia, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
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17
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Barroso A, Giménez E, Benavente F, Barbosa J, Sanz-Nebot V. Classification of congenital disorders of glycosylation based on analysis of transferrin glycopeptides by capillary liquid chromatography-mass spectrometry. Talanta 2016; 160:614-623. [PMID: 27591658 DOI: 10.1016/j.talanta.2016.07.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/22/2016] [Accepted: 07/24/2016] [Indexed: 01/30/2023]
Abstract
In this work, we describe a multivariate data analysis approach for data exploration and classification of the complex and large data sets generated to study the alteration of human transferrin (Tf) N-glycopeptides in patients with congenital disorders of glycosylation (CDG). Tf from healthy individuals and two types of CDG patients (CDG-I and CDG-II) is purified by immunoextraction from serum samples before trypsin digestion and separation by capillary liquid chromatography mass spectrometry (CapLC-MS). Following a targeted data analysis approach, partial least squares discriminant analysis (PLS-DA) is applied to the relative abundance of Tf glycopeptide glycoforms obtained after integration of the extracted ion chromatograms of the different samples. The performance of PLS-DA for classification of the different samples and for providing a novel insight into Tf glycopeptide glycoforms alteration in CDGs is demonstrated. Only six out of fourteen of the detected glycoforms are enough for an accurate classification. This small glycoform set may be considered a sensitive and specific novel biomarker panel for CDGs.
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Affiliation(s)
- Albert Barroso
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
| | - José Barbosa
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
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18
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Farrés M, Piña B, Tauler R. LC-MS based metabolomics and chemometrics study of the toxic effects of copper on Saccharomyces cerevisiae. Metallomics 2016; 8:790-8. [DOI: 10.1039/c6mt00021e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Copper containing fungicides are used to protect vineyards from fungal infections.
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Affiliation(s)
- Mireia Farrés
- Institute of Environmental Assessment and Water Research (IDAEA)
- Spanish Council for Scientific Research (CSIC)
- 08034 Barcelona, Spain
| | - Benjamí Piña
- Institute of Environmental Assessment and Water Research (IDAEA)
- Spanish Council for Scientific Research (CSIC)
- 08034 Barcelona, Spain
| | - Romà Tauler
- Institute of Environmental Assessment and Water Research (IDAEA)
- Spanish Council for Scientific Research (CSIC)
- 08034 Barcelona, Spain
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19
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Navarro-Reig M, Jaumot J, García-Reiriz A, Tauler R. Evaluation of changes induced in rice metabolome by Cd and Cu exposure using LC-MS with XCMS and MCR-ALS data analysis strategies. Anal Bioanal Chem 2015; 407:8835-47. [PMID: 26403240 DOI: 10.1007/s00216-015-9042-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/07/2015] [Accepted: 09/10/2015] [Indexed: 12/25/2022]
Abstract
The comprehensive analysis of untargeted metabolomics data acquired using LC-MS is still a major challenge. Different data analysis tools have been developed in recent years such as XCMS (various forms (X) of chromatography mass spectrometry) and multivariate curve resolution alternating least squares (MCR-ALS)-based strategies. In this work, metabolites extracted from rice tissues cultivated in an environmental test chamber were subjected to untargeted full-scan LC-MS analysis, and the obtained data sets were analyzed using XCMS and MCR-ALS. These approaches were compared in the investigation of the effects of copper and cadmium exposure on rice tissue (roots and aerial parts) samples. Both methods give, as a result of their application, the whole set of resolved elution and spectra profiles of the extracted metabolites in control and metal-treated samples, as well as the values of their corresponding chromatographic peak areas. The effects caused by the two considered metals on rice samples were assessed by further chemometric analysis and statistical evaluation of these peak area values. Results showed that there was a statistically significant interaction between the considered factors (type of metal of treatment and tissue). Also, the discrimination of the samples according to both factors was possible. A tentative identification of the most discriminant metabolites (biomarkers) was assessed. It is finally concluded that both XCMS- and MCR-ALS-based strategies provided similar results in all the considered cases despite the completely different approaches used by these two methods in the chromatographic peak resolution and detection strategies. Finally, advantages and disadvantages of using these two methods are discussed. Graphical Abstract Summary of the workflow for untargeted metabolomics using the compared approaches.
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Affiliation(s)
- Meritxell Navarro-Reig
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Joaquim Jaumot
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain.
| | - Alejandro García-Reiriz
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain.,Departamento de Química Analítica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Instituto de Química Rosario (IQUIR-CONICET), Suipacha 531, Rosario, S2002LRK, Argentina
| | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
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