1
|
Zweigle J, Bugsel B, Fabregat-Palau J, Zwiener C. PFΔScreen - an open-source tool for automated PFAS feature prioritization in non-target HRMS data. Anal Bioanal Chem 2024; 416:349-362. [PMID: 38030884 PMCID: PMC10761406 DOI: 10.1007/s00216-023-05070-2] [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: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a huge group of anthropogenic chemicals with unique properties that are used in countless products and applications. Due to the high stability of their C-F bonds, PFAS or their transformation products (TPs) are persistent in the environment, leading to ubiquitous detection in various samples worldwide. Since PFAS are industrial chemicals, the availability of authentic PFAS reference standards is limited, making non-target screening (NTS) approaches based on high-resolution mass spectrometry (HRMS) necessary for a more comprehensive characterization. NTS usually is a time-consuming process, since only a small fraction of the detected chemicals can be identified. Therefore, efficient prioritization of relevant HRMS signals is one of the most crucial steps. We developed PFΔScreen, a Python-based open-source tool with a simple graphical user interface (GUI) to perform efficient feature prioritization using several PFAS-specific techniques such as the highly promising MD/C-m/C approach, Kendrick mass defect analysis, diagnostic fragments (MS2), fragment mass differences (MS2), and suspect screening. Feature detection from vendor-independent MS raw data (mzML, data-dependent acquisition) is performed via pyOpenMS (or custom feature lists) with subsequent calculations for prioritization and identification of PFAS in both HPLC- and GC-HRMS data. The PFΔScreen workflow is presented on four PFAS-contaminated agricultural soil samples from south-western Germany. Over 15 classes of PFAS (more than 80 single compounds with several isomers) could be identified, including four novel classes, potentially TPs of the precursors fluorotelomer mercapto alkyl phosphates (FTMAPs). PFΔScreen can be used within the Python environment and is easily automatically installable and executable on Windows. Its source code is freely available on GitHub ( https://github.com/JonZwe/PFAScreen ).
Collapse
Affiliation(s)
- Jonathan Zweigle
- Environmental Analytical Chemistry, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076, Tübingen, Germany.
| | - Boris Bugsel
- Environmental Analytical Chemistry, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076, Tübingen, Germany
| | - Joel Fabregat-Palau
- Hydrogeochemistry, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076, Tübingen, Germany
| | - Christian Zwiener
- Environmental Analytical Chemistry, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076, Tübingen, Germany.
| |
Collapse
|
2
|
Molecular signature of renal cell carcinoma by means of a multiplatform metabolomics analysis. Biochem Biophys Rep 2022; 31:101318. [PMID: 35967759 PMCID: PMC9363947 DOI: 10.1016/j.bbrep.2022.101318] [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: 04/27/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 12/30/2022] Open
Abstract
Renal cell carcinoma (RCC) is a disease with no specific diagnostic method or treatment. Thus, the evaluation of novel diagnostic tools or treatment possibilities is essential. In this study, a multiplatform untargeted metabolomics analysis of urine was applied to search for a metabolic pattern specific for RCC, which could enable comprehensive assessment of its biochemical background. Thirty patients with diagnosed RCC and 29 healthy volunteers were involved in the first stage of the study. Initially, the utility of the application of the selected approach was checked for RCC with no differentiation for cancer subtypes. In the second stage, this approach was used to study clear cell renal cell carcinoma (ccRCC) in 38 ccRCC patients and 38 healthy volunteers. Three complementary analytical platforms were used: reversed-phase liquid chromatography coupled with time-of-flight mass spectrometry (RP-HPLC-TOF/MS), capillary electrophoresis coupled with time-of-flight mass spectrometry (CE-TOF/MS), and gas chromatography triple quadrupole mass spectrometry (GC-QqQ/MS). As a result of urine sample analyses, two panels of metabolites specific for RCC and ccRCC were selected. Disruptions in amino acid, lipid, purine, and pyrimidine metabolism, the TCA cycle and energetic processes were observed. The most interesting differences were observed for modified nucleosides. This is the first time that the levels of these compounds were found to be changed in RCC and ccRCC patients, providing a framework for further studies. Moreover, the application of the CE-MS technique enabled the determination of statistically significant changes in symmetric dimethylarginine (SDMA) in RCC. Multiplatform untargeted metabolomics analysis was applied for selection of tentative diagnostic indicators of RCC. LC-MS, GC-MS and CE-MS techniques were utilized for analysis of urine samples collected from RCC and ccRCC patients. Alterations in amino acid, purine, and pyrimidine metabolism, as well as TCA cycle and energy processes, were observed.
Collapse
|
3
|
López-López Á, Ciborowski M, Niklinski J, Barbas C, López-Gonzálvez Á. Optimization of capillary electrophoresis coupled to negative mode electrospray ionization-mass spectrometry using polyvinyl alcohol coated capillaries. Application to a study on non-small cell lung cancer. Anal Chim Acta 2022; 1226:340259. [DOI: 10.1016/j.aca.2022.340259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/13/2022] [Accepted: 08/11/2022] [Indexed: 11/01/2022]
|
4
|
Boutet S, Barreda L, Perreau F, Totozafy JC, Mauve C, Gakière B, Delannoy E, Martin-Magniette ML, Monti A, Lepiniec L, Zanetti F, Corso M. Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:147-165. [PMID: 34997644 DOI: 10.1111/tpj.15662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Stéphanie Boutet
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Léa Barreda
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - François Perreau
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Jean-Chrisologue Totozafy
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Caroline Mauve
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
| | - Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405, Orsay, France
- UMR MIA-Paris, AgroParisTech, INRAE, Université Paris-Saclay, 75005, Paris, France
| | - Andrea Monti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Loïc Lepiniec
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Federica Zanetti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Massimiliano Corso
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| |
Collapse
|
5
|
Albóniga OE, Jiménez D, Sánchez-Conde M, Vizcarra P, Ron R, Herrera S, Martínez-Sanz J, Moreno E, Moreno S, Barbas C, Serrano-Villar S. Metabolic Snapshot of Plasma Samples Reveals New Pathways Implicated in SARS-CoV-2 Pathogenesis. J Proteome Res 2022; 21:623-634. [PMID: 35133846 DOI: 10.1021/acs.jproteome.1c00786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of severe disease. Here, we used untargeted metabolomics to examine novel metabolic pathways related to SARS-CoV-2 susceptibility and COVID-19 clinical severity using capillary electrophoresis coupled to a time-of-flight mass spectrometer (CE-TOF-MS) in plasma samples. We included 27 patients with confirmed COVID-19 and 29 healthcare workers heavily exposed to SARS-CoV-2 but with low susceptibility to infection ("nonsusceptible"). We found a total of 42 metabolites of SARS-CoV-2 susceptibility or COVID-19 clinical severity. We report the discovery of new plasma biomarkers for COVID-19 that provide mechanistic explanations for the clinical consequences of SARS-CoV-2, including mitochondrial and liver dysfunction as a consequence of hypoxemia (citrulline, citric acid, and 3-aminoisobutyric acid (BAIBA)), energy production and amino acid catabolism (phenylalanine and histidine), and endothelial dysfunction and thrombosis (citrulline, asymmetric dimethylarginine (ADMA), and 2-aminobutyric acid (2-AB)), and we found interconnections between these pathways. In summary, in this first report several metabolic pathways implicated in SARS-CoV-2 susceptibility and COVID-19 clinical progression were found by CE-MS based metabolomics that could be developed as biomarkers of COVID-19.
Collapse
Affiliation(s)
- Oihane E Albóniga
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28660 Madrid, Spain
| | - Daniel Jiménez
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Matilde Sánchez-Conde
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Pilar Vizcarra
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Raquel Ron
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Sabina Herrera
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Javier Martínez-Sanz
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Elena Moreno
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Santiago Moreno
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28660 Madrid, Spain
| | - Sergio Serrano-Villar
- Servicio de Enfermedades Infecciosas, IRYCIS, Hospital Universitario Ramón y Cajal and CIBERInf, Carretera de Colmenar Viejo km 9.100, 28034 Madrid, Spain
| |
Collapse
|
6
|
Wasito H, Causon T, Hann S. Alternating in-source fragmentation with single-stage high-resolution mass spectrometry with high annotation confidence in non-targeted metabolomics. Talanta 2022; 236:122828. [PMID: 34635218 DOI: 10.1016/j.talanta.2021.122828] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023]
Abstract
Non-targeted metabolomics is increasingly applied in various applications for understanding biological processes and finding novel biomarkers in living organisms. However, high-confidence identity confirmation of metabolites in complex biological samples is still a significant bottleneck, especially when using single-stage mass analysers. In the current study, a complete workflow for alternating in-source fragmentation on a time-of-flight mass spectrometry (TOFMS) instrument for non-targeted metabolomics is presented. Hydrophilic interaction liquid chromatography (HILIC) was employed to assess polar metabolites in yeast following ESI parameter optimization using experimental design principles, which revealed the key influence of fragmentor voltage for this application. Datasets from alternating in-source fragmentation high resolution mass spectrometry (HRMS) were evaluated using open-source data processing tools combined with public reference mass spectral databases. The significant influence of the selected fragmentor voltages on the abundance of the primary analyte ion of interest and the extent of in-source fragmentation allowed an optimum selection of qualifier fragments for the different metabolites. The new acquisition and evaluation workflow was implemented for the non-targeted analysis of yeast extract samples whereby more than 130 metabolites were putatively annotated with more than 40% considered to be of high confidence. The presented workflow contains a fully elaborated acquisition and evaluation methodology using alternating in-source fragmentor voltages suitable for peak annotation and metabolite identity confirmation for non-targeted metabolomics applications performed on a single-stage HRMS platform.
Collapse
Affiliation(s)
- Hendri Wasito
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria; Department of Pharmacy, Faculty of Health Sciences, Jenderal Soedirman University, Dr. Soeparno Street, 53122, Purwokerto, Indonesia
| | - Tim Causon
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria.
| |
Collapse
|
7
|
Wu M, Lin R, Yin J, Ding H, Han L, Yang W, Bie S, Wang C, Zheng W, Song X, Ma B, Yu H, Li Z. The multicomponent characterization of Shuanghe decoction by dimension-enhanced data-independent HDMSE: Focusing on the performance comparison between MSE and HDMSE. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Manzi M, Palazzo M, Knott ME, Beauseroy P, Yankilevich P, Giménez MI, Monge ME. Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma. J Proteome Res 2020; 20:841-857. [PMID: 33207877 DOI: 10.1021/acs.jproteome.0c00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell renal cell carcinoma (ccRCC) stages I, II, III, and IV (n = 112) and controls (n = 52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross-validation and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2), identified with level 1 exhibited significantly lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
Collapse
Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina.,Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Palazzo
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - Pierre Beauseroy
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Isabel Giménez
- Departamento de Diagnóstico y Tratamiento, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199ABB CABA, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| |
Collapse
|
10
|
Abstract
Untargeted metabolomics aims to quantify the complete set of metabolites within a biological system, most commonly by liquid chromatography/mass spectrometry (LC/MS). Since nearly the inception of the field, compound identification has been widely recognized as the rate-limiting step of the experimental workflow. In spite of exponential increases in the size of metabolomic databases, which now contain experimental MS/MS spectra for over a half a million reference compounds, chemical structures still cannot be confidently assigned to many signals in a typical LC/MS dataset. The purpose of this Perspective is to consider why identification rates continue to be low in untargeted metabolomics. One rationalization is that many naturally occurring metabolites detected by LC/MS are true "novel" compounds that have yet to be incorporated into metabolomic databases. An alternative possibility, however, is that research data do not provide database matches because of informatic artifacts, chemical contaminants, and signal redundancies. Increasing evidence suggests that, for at least some sample types, many unidentifiable signals in untargeted metabolomics result from the latter rather than new compounds originating from the specimen being measured. The implications of these observations on chemical discovery in untargeted metabolomics are discussed.
Collapse
Affiliation(s)
- Miriam Sindelar
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gary J. Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| |
Collapse
|
11
|
Mamani-Huanca M, Gradillas A, Gil de la Fuente A, López-Gonzálvez Á, Barbas C. Unveiling the Fragmentation Mechanisms of Modified Amino Acids as the Key for Their Targeted Identification. Anal Chem 2020; 92:4848-4857. [DOI: 10.1021/acs.analchem.9b04313] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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
| | - 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
| | - 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
| | - 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
| | - 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
| |
Collapse
|
12
|
van Mever M, Hankemeier T, Ramautar R. CE-MS for anionic metabolic profiling: An overview of methodological developments. Electrophoresis 2019; 40:2349-2359. [PMID: 31106868 PMCID: PMC6771621 DOI: 10.1002/elps.201900115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/24/2022]
Abstract
The efficient profiling of highly polar and charged metabolites in biological samples remains a huge analytical challenge in metabolomics. Over the last decade, new analytical techniques have been developed for the selective and sensitive analysis of polar ionogenic compounds in various matrices. Still, the analysis of such compounds, notably for acidic ionogenic metabolites, remains a challenging endeavor, even more when the available sample size becomes an issue for the total analytical workflow. In this paper, we give an overview of the possibilities of capillary electrophoresis-mass spectrometry (CE-MS) for anionic metabolic profiling by focusing on main methodological developments. Attention is paid to the development of improved separation conditions and new interfacing designs in CE-MS for anionic metabolic profiling. A complete overview of all CE-MS-based methods developed for this purpose is provided in table format (Table 1) which includes information on sample type, separation conditions, mass analyzer and limits of detection (LODs). Selected applications are discussed to show the utility of CE-MS for anionic metabolic profiling, especially for small-volume biological samples. On the basis of the examination of the reported literature in this specific field, we conclude that there is still room for the design of a highly sensitive and reliable CE-MS method for anionic metabolic profiling. A rigorous validation and the availability of standard operating procedures would be highly favorable in order to make CE-MS an alternative, viable analytical technique for metabolomics.
Collapse
Affiliation(s)
- Marlien van Mever
- Biomedical Microscale AnalyticsLeiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Thomas Hankemeier
- Analytical BioSciences & MetabolomicsLeiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Rawi Ramautar
- Biomedical Microscale AnalyticsLeiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| |
Collapse
|
13
|
Godzien J, Kalaska B, Adamska-Patruno E, Siroka J, Ciborowski M, Kretowski A, Barbas C. Oxidized glycerophosphatidylcholines in diabetes through non-targeted metabolomics: Their annotation and biological meaning. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1120:62-70. [DOI: 10.1016/j.jchromb.2019.04.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
|
14
|
Gonzalez-Riano C, León-Espinosa G, Regalado-Reyes M, García A, DeFelipe J, Barbas C. Metabolomic Study of Hibernating Syrian Hamster Brains: In Search of Neuroprotective Agents. J Proteome Res 2019; 18:1175-1190. [DOI: 10.1021/acs.jproteome.8b00816] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Gonzalo León-Espinosa
- Laboratorio Cajal de Circuitos Corticales (CTB), Universidad Politécnica de Madrid, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Instituto Cajal (CSIC), Avenida Doctor Arce 37, 28002 Madrid, Spain
| | - Mamen Regalado-Reyes
- Laboratorio Cajal de Circuitos Corticales (CTB), Universidad Politécnica de Madrid, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | | | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales (CTB), Universidad Politécnica de Madrid, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Instituto Cajal (CSIC), Avenida Doctor Arce 37, 28002 Madrid, Spain
- CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Calle de Valderrebollo, 5, 28031 Madrid, Spain
| | | |
Collapse
|
15
|
Rojo D, Barbas C, López-Gonzálvez Á. Metabolomics Analysis of Leishmania by Capillary Electrophoresis and Mass Spectrometry. Methods Mol Biol 2019; 1859:253-260. [PMID: 30421234 DOI: 10.1007/978-1-4939-8757-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Capillary electrophoresis coupled to mass spectrometry is an analytical platform ideal for the analysis of ionic or polar metabolites. It constitutes a perfect complement to reversed-phase liquid chromatography, offering a good alternative to polar stationary phases where reproducibility is not guaranteed. Herein, we describe a robust standardized methodology for the fingerprinting analysis of Leishmania, a taxonomic genus which comprises more than 20 protozoa species.
Collapse
MESH Headings
- Chromatography, High Pressure Liquid/instrumentation
- Chromatography, High Pressure Liquid/methods
- Chromatography, Reverse-Phase/instrumentation
- Chromatography, Reverse-Phase/methods
- Electrophoresis, Capillary/instrumentation
- Electrophoresis, Capillary/methods
- Leishmania/metabolism
- Metabolomics/instrumentation
- Metabolomics/methods
- Reproducibility of Results
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
Collapse
Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanállisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanállisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centro de Metabolómica y Bioanállisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain.
| |
Collapse
|
16
|
Abstract
Although capillary electrophoresis (CE) coupled to mass spectrometry (MS) is a separation technique not extensively implemented, it offers differential possibilities in the study of polar and ionic metabolites in complex matrices with minimum sample treatment. However, in order to get successful results, some efforts at early stages and following specific recommendations are necessary.In this chapter, we describe our updated and well-tested methods for untargeted metabolomics using CE-MS-TOF for common biological samples: urine, serum or plasma, feces, tissues, and cells. Sample treatment, as well as separation and detection conditions are described in detail and other steps in the workflow for untargeted metabolomics are also explained. Special attention is paid to instrumental setup and advices for daily practice.Characteristic electropherograms obtained with each type of sample are depicted as well as groups of metabolites easily measured by this technique. Their global or individual comparisons have been given undoubtedly important information to unveil altered metabolic pathways, diagnosis, and prognosis or biomarker discovery in the study of diseases or conditions over decades.
Collapse
|
17
|
Gathungu RM, Larrea P, Sniatynski MJ, Marur VR, Bowden JA, Koelmel JP, Starke-Reed P, Hubbard VS, Kristal BS. Optimization of Electrospray Ionization Source Parameters for Lipidomics To Reduce Misannotation of In-Source Fragments as Precursor Ions. Anal Chem 2018; 90:13523-13532. [PMID: 30265528 PMCID: PMC6297073 DOI: 10.1021/acs.analchem.8b03436] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipidomics requires the accurate annotation of lipids in complex samples to enable determination of their biological relevance. We demonstrate that unintentional in-source fragmentation (ISF, common in lipidomics) generates ions that have identical masses to other lipids. Lysophosphatidylcholines (LPC), for example, generate in-source fragments with the same mass as free fatty acids and lysophosphatidylethanolamines (LPE). The misannotation of in-source fragments as true lipids is particularly insidious in complex matrixes since most masses are initially unannotated and comprehensive lipid standards are unavailable. Indeed, we show such LPE/LPC misannotations are incorporated in the data submitted to the National Institute of Standards and Technology (NIST) interlaboratory comparison exercise. Computer simulations exhaustively identified potential misannotations. The selection of in-source fragments of highly abundant lipids as features, instead of the correct recognition of trace lipids, can potentially lead to (i) missing the biologically relevant lipids (i.e., a false negative) and/or (ii) incorrect assignation of a phenotype to an incorrect lipid (i.e., false positive). When ISF is not eliminated in the negative ion mode, ∼40% of the 100 most abundant masses corresponding to unique phospholipids measured in plasma were artifacts from ISF. We show that chromatographic separation and ion intensity considerations assist in distinguishing precursor ions from in-source fragments, suggesting ISF may be especially problematic when complex samples are analyzed via shotgun lipidomics. We also conduct a systematic evaluation of electrospray ionization (ESI) source parameters on an Exactive equipped with a heated electrospray ionization (HESI-II) source with the objective of obtaining uniformly appropriate source conditions for a wide range of lipids, while, at the same time, reducing in-source fragmentation.
Collapse
Affiliation(s)
- Rose M. Gathungu
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Pablo Larrea
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Matthew J. Sniatynski
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Vasant R. Marur
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - John A. Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610
- National Institute of Standards and Technology, Hollings Marine Laboratory, Charleston, SC 29412
| | - Jeremy P. Koelmel
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610
| | - Pamela Starke-Reed
- Deputy Director, NIH Division of Nutrition Research Coordination, Bethesda, MD 20892
| | - Van S. Hubbard
- Director, NIH Division of Nutrition Research Coordination, Bethesda, MD 20892
| | - Bruce S. Kristal
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
18
|
Binek A, Rojo D, Godzien J, Rupérez FJ, Nuñez V, Jorge I, Ricote M, Vázquez J, Barbas C. Flow Cytometry Has a Significant Impact on the Cellular Metabolome. J Proteome Res 2018; 18:169-181. [PMID: 30362351 DOI: 10.1021/acs.jproteome.8b00472] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyze the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signaling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry.
Collapse
Affiliation(s)
- Aleksandra Binek
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
| | - Joanna Godzien
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
| | - Francisco Javier Rupérez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
| | - Vanessa Nuñez
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1
| | - Inmaculada Jorge
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1.,CIBER de Enfermedades Cardiovasculares (CIBER CV), Madrid 28029 , Spain
| | - Mercedes Ricote
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1
| | - Jesús Vázquez
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1.,CIBER de Enfermedades Cardiovasculares (CIBER CV), Madrid 28029 , Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
| |
Collapse
|
19
|
Seitzer PM, Searle BC. Incorporating In-Source Fragment Information Improves Metabolite Identification Accuracy in Untargeted LC–MS Data Sets. J Proteome Res 2018; 18:791-796. [DOI: 10.1021/acs.jproteome.8b00601] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Phillip M. Seitzer
- Proteome Software, 1340 Southwest Bertha Boulevard Suite 10, Portland, Oregon 97219, United States
| | - Brian C. Searle
- Proteome Software, 1340 Southwest Bertha Boulevard Suite 10, Portland, Oregon 97219, United States
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
20
|
Armitage EG, Godzien J, Peña I, López-Gonzálvez Á, Angulo S, Gradillas A, Alonso-Herranz V, Martín J, Fiandor JM, Barrett MP, Gabarro R, Barbas C. Metabolic Clustering Analysis as a Strategy for Compound Selection in the Drug Discovery Pipeline for Leishmaniasis. ACS Chem Biol 2018; 13:1361-1369. [PMID: 29671577 DOI: 10.1021/acschembio.8b00204] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A lack of viable hits, increasing resistance, and limited knowledge on mode of action is hindering drug discovery for many diseases. To optimize prioritization and accelerate the discovery process, a strategy to cluster compounds based on more than chemical structure is required. We show the power of metabolomics in comparing effects on metabolism of 28 different candidate treatments for Leishmaniasis (25 from the GSK Leishmania box, two analogues of Leishmania box series, and amphotericin B as a gold standard treatment), tested in the axenic amastigote form of Leishmania donovani. Capillary electrophoresis-mass spectrometry was applied to identify the metabolic profile of Leishmania donovani, and principal components analysis was used to cluster compounds on potential mode of action, offering a medium throughput screening approach in drug selection/prioritization. The comprehensive and sensitive nature of the data has also made detailed effects of each compound obtainable, providing a resource to assist in further mechanistic studies and prioritization of these compounds for the development of new antileishmanial drugs.
Collapse
Affiliation(s)
- Emily G. Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Imanol Peña
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Santiago Angulo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Vanesa Alonso-Herranz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Julio Martín
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Jose M. Fiandor
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Raquel Gabarro
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| |
Collapse
|
21
|
Armitage EG, Alqaisi AQI, Godzien J, Peña I, Mbekeani AJ, Alonso-Herranz V, López-Gonzálvez Á, Martín J, Gabarro R, Denny PW, Barrett MP, Barbas C. Complex Interplay between Sphingolipid and Sterol Metabolism Revealed by Perturbations to the Leishmania Metabolome Caused by Miltefosine. Antimicrob Agents Chemother 2018; 62:e02095-17. [PMID: 29463533 PMCID: PMC5923112 DOI: 10.1128/aac.02095-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/21/2018] [Indexed: 12/24/2022] Open
Abstract
With the World Health Organization reporting over 30,000 deaths and 200,000 to 400,000 new cases annually, visceral leishmaniasis is a serious disease affecting some of the world's poorest people. As drug resistance continues to rise, there is a huge unmet need to improve treatment. Miltefosine remains one of the main treatments for leishmaniasis, yet its mode of action (MoA) is still unknown. Understanding the MoA of this drug and parasite response to treatment could help pave the way for new and more successful treatments for leishmaniasis. A novel method has been devised to study the metabolome and lipidome of Leishmania donovani axenic amastigotes treated with miltefosine. Miltefosine caused a dramatic decrease in many membrane phospholipids (PLs), in addition to amino acid pools, while sphingolipids (SLs) and sterols increased. Leishmania major promastigotes devoid of SL biosynthesis through loss of the serine palmitoyl transferase gene (ΔLCB2) were 3-fold less sensitive to miltefosine than wild-type (WT) parasites. Changes in the metabolome and lipidome of miltefosine-treated L. major mirrored those of L. donovani A lack of SLs in the ΔLCB2 mutant was matched by substantial alterations in sterol content. Together, these data indicate that SLs and ergosterol are important for miltefosine sensitivity and, perhaps, MoA.
Collapse
Affiliation(s)
- Emily G Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Tres Cantos, Madrid, Spain
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences & Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Amjed Q I Alqaisi
- Department of Biosciences, Durham University, Lower Mountjoy, Durham, United Kingdom
- University of Baghdad, College of Science, Biology Department, Baghdad, Iraq
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Imanol Peña
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Tres Cantos, Madrid, Spain
| | - Alison J Mbekeani
- Department of Biosciences, Durham University, Lower Mountjoy, Durham, United Kingdom
| | - Vanesa Alonso-Herranz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Julio Martín
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Tres Cantos, Madrid, Spain
| | - Raquel Gabarro
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Tres Cantos, Madrid, Spain
| | - Paul W Denny
- Department of Biosciences, Durham University, Lower Mountjoy, Durham, United Kingdom
| | - Michael P Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences & Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| |
Collapse
|
22
|
Godzien J, Gil de la Fuente A, Otero A, Barbas C. Metabolite Annotation and Identification. COMPREHENSIVE ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/bs.coac.2018.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
23
|
Mrzic A, Lermyte F, Vu TN, Valkenborg D, Laukens K. InSourcerer: a high-throughput method to search for unknown metabolite modifications by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1396-1404. [PMID: 28569011 DOI: 10.1002/rcm.7910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Using mass spectrometry, the analysis of known metabolite structures has become feasible in a systematic high-throughput fashion. Nevertheless, the identification of previously unknown structures remains challenging, partially because many unidentified variants originate from known molecules that underwent unexpected modifications. Here, we present a method for the discovery of unknown metabolite modifications and conjugate metabolite isoforms in a high-throughput fashion. METHODS The method is based on user-controlled in-source fragmentation which is used to induce loss of weakly bound modifications. This is followed by the comparison of product ions from in-source fragmentation and collision-induced dissociation (CID). Diagonal MS2 -MS3 matching allows the detection of unknown metabolite modifications, as well as substructure similarities. As the method relies heavily on the advantages of in-source fragmentation and its ability to 'magically' elucidate unknown modification, we have named it inSourcerer as a portmanteau of in-source and sorcerer. RESULTS The method was evaluated using a set of 15 different cytokinin standards. Product ions from in-source fragmentation and CID were compared. Hierarchical clustering revealed that good matches are due to the presence of common substructures. Plant leaf extract, spiked with a mix of all 15 standards, was used to demonstrate the method's ability to detect these standards in a complex mixture, as well as confidently identify compounds already present in the plant material. CONCLUSIONS Here we present a method that incorporates a classic liquid chromatography/mass spectrometry (LC/MS) workflow with fragmentation models and computational algorithms. The assumptions upon which the concept of the method was built were shown to be valid and the method showed that in-source fragmentation can be used to pinpoint structural similarities and indicate the occurrence of a modification.
Collapse
Affiliation(s)
- Aida Mrzic
- Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
- Biomedical Informatics Research Network Antwerpen (biomina), University of Antwerp / Antwerp University Hospital, Antwerpen, Belgium
| | - Frederik Lermyte
- Applied Bio & Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
- UA-VITO Center for Proteomics, University of Antwerp, Antwerpen, Belgium
- Department of Chemistry, University of Antwerp, Antwerpen, Belgium
| | - Trung Nghia Vu
- Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
- Biomedical Informatics Research Network Antwerpen (biomina), University of Antwerp / Antwerp University Hospital, Antwerpen, Belgium
| | - Dirk Valkenborg
- Applied Bio & Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
- UA-VITO Center for Proteomics, University of Antwerp, Antwerpen, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
- Biomedical Informatics Research Network Antwerpen (biomina), University of Antwerp / Antwerp University Hospital, Antwerpen, Belgium
| |
Collapse
|
24
|
Gil de la Fuente A, Grace Armitage E, Otero A, Barbas C, Godzien J. Differentiating signals to make biological sense - A guide through databases for MS-based non-targeted metabolomics. Electrophoresis 2017; 38:2242-2256. [PMID: 28426136 DOI: 10.1002/elps.201700070] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/17/2017] [Accepted: 03/17/2017] [Indexed: 12/21/2022]
Abstract
Metabolite identification is one of the most challenging steps in metabolomics studies and reflects one of the greatest bottlenecks in the entire workflow. The success of this step determines the success of the entire research, therefore the quality at which annotations are given requires special attention. A variety of tools and resources are available to aid metabolite identification or annotation, offering different and often complementary functionalities. In preparation for this article, almost 50 databases were reviewed, from which 17 were selected for discussion, chosen for their online ESI-MS functionality. The general characteristics and functions of each database is discussed in turn, considering the advantages and limitations of each along with recommendations for optimal use of each tool, as derived from experiences encountered at the Centre for Metabolomics and Bioanalysis (CEMBIO) in Madrid. These databases were evaluated considering their utility in non-targeted metabolomics, including aspects such as identifier assignment, structural assignment and interpretation of results.
Collapse
Affiliation(s)
- Alberto Gil de la Fuente
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain.,Department of Information Technology, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Emily Grace Armitage
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Abraham Otero
- Department of Information Technology, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, Spain
| |
Collapse
|
25
|
Capillary electrophoresis mass spectrometry as a tool for untargeted metabolomics. Bioanalysis 2017; 9:99-130. [PMID: 27921456 DOI: 10.4155/bio-2016-0216] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Highly polar and ionic metabolites, such as sugars, most amino acids, organic acids or nucleotides are not retained by conventional reversed-phase LC columns and polar stationary phases and hydrophilic-interaction LC lacks of robustness, which is still limiting their applications for untargeted metabolomics where reproducibility is a must. Biological samples such as blood, urine or even tissues include many hydrophilic compounds secreted from cells, their analysis is essential for biomarker discovery, disease progression or treatment effects. This review focuses on CE coupled to MS as a mature technique for untargeted metabolomics including sample pretreatment, types of matrices, analytical methods, applications and data treatment strategies for polar compound analysis in biological matrices. The main applications and results of CE-MS in untargeted metabolomics are discussed and presented in a tabulated format.
Collapse
|
26
|
Gonzalez-Riano C, Garcia A, Barbas C. Metabolomics studies in brain tissue: A review. J Pharm Biomed Anal 2016; 130:141-168. [PMID: 27451335 DOI: 10.1016/j.jpba.2016.07.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022]
Abstract
Brain is still an organ with a composition to be discovered but beyond that, mental disorders and especially all diseases that curse with dementia are devastating for the patient, the family and the society. Metabolomics can offer an alternative tool for unveiling new insights in the discovery of new treatments and biomarkers of mental disorders. Until now, most of metabolomic studies have been based on biofluids: serum/plasma or urine, because brain tissue accessibility is limited to animal models or post mortem studies, but even so it is crucial for understanding the pathological processes. Metabolomics studies of brain tissue imply several challenges due to sample extraction, along with brain heterogeneity, sample storage, and sample treatment for a wide coverage of metabolites with a wide range of concentrations of many lipophilic and some polar compounds. In this review, the current analytical practices for target and non-targeted metabolomics are described and discussed with emphasis on critical aspects: sample treatment (quenching, homogenization, filtration, centrifugation and extraction), analytical methods, as well as findings considering the used strategies. Besides that, the altered analytes in the different brain regions have been associated with their corresponding pathways to obtain a global overview of their dysregulation, trying to establish the link between altered biological pathways and pathophysiological conditions.
Collapse
Affiliation(s)
- Carolina Gonzalez-Riano
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte 28668, Madrid, Spain
| | - Antonia Garcia
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte 28668, Madrid, Spain.
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte 28668, Madrid, Spain
| |
Collapse
|