Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts
Metabolomics, understood as the science that manages the study of compounds from the metabolism, is an essential tool for deciphering metabolic changes in disease. The experiments rely on the use of high-throughput analytical techniques such as liquid chromatography coupled to mass spectrometry (LC-...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-10-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/9/11/247 |
| _version_ | 1818896909261078528 |
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| author | Juan Rodríguez-Coira María I Delgado-Dolset David Obeso Mariana Dolores-Hernández Guillermo Quintás Santiago Angulo Domingo Barber Teresa Carrillo María M. Escribese Alma Villaseñor |
| author_facet | Juan Rodríguez-Coira María I Delgado-Dolset David Obeso Mariana Dolores-Hernández Guillermo Quintás Santiago Angulo Domingo Barber Teresa Carrillo María M. Escribese Alma Villaseñor |
| author_sort | Juan Rodríguez-Coira |
| collection | DOAJ |
| description | Metabolomics, understood as the science that manages the study of compounds from the metabolism, is an essential tool for deciphering metabolic changes in disease. The experiments rely on the use of high-throughput analytical techniques such as liquid chromatography coupled to mass spectrometry (LC-ToF MS). This hyphenation has brought positive aspects such as higher sensitivity, specificity and the extension of the metabolome coverage in a single run. The analysis of a high number of samples in a single batch is currently not always feasible due to technical and practical issues (i.e., a drop of the MS signal) which result in the MS stopping during the experiment obtaining more than a single sample batch. In this situation, careful data treatment is required to enable an accurate joint analysis of multi-batch data sets. This paper summarizes the analytical strategies in large-scale metabolomic experiments; special attention has been given to QC preparation troubleshooting and data treatment. Moreover, labeled internal standards analysis and their aim in data treatment, and data normalization procedures (intra- and inter-batch) are described. These concepts are exemplified using a cohort of 165 patients from a study in asthma. |
| first_indexed | 2024-12-19T19:07:46Z |
| format | Article |
| id | doaj.art-c8223353307149eaa9e9fbd14a692ad8 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-12-19T19:07:46Z |
| publishDate | 2019-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-c8223353307149eaa9e9fbd14a692ad82022-12-21T20:09:24ZengMDPI AGMetabolites2218-19892019-10-0191124710.3390/metabo9110247metabo9110247Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big CohortsJuan Rodríguez-Coira0María I Delgado-Dolset1David Obeso2Mariana Dolores-Hernández3Guillermo Quintás4Santiago Angulo5Domingo Barber6Teresa Carrillo7María M. Escribese8Alma Villaseñor9CEMBIO, Centro de Excelencia en Metabolómica y Bioanálisis, Facultad de Farmacia, Universidad San Pablo CEU, 28668 Madrid, SpainCEMBIO, Centro de Excelencia en Metabolómica y Bioanálisis, Facultad de Farmacia, Universidad San Pablo CEU, 28668 Madrid, SpainCEMBIO, Centro de Excelencia en Metabolómica y Bioanálisis, Facultad de Farmacia, Universidad San Pablo CEU, 28668 Madrid, SpainCEMBIO, Centro de Excelencia en Metabolómica y Bioanálisis, Facultad de Farmacia, Universidad San Pablo CEU, 28668 Madrid, SpainHealth and Biomedicine, Leitat Technological Center, 08028 Barcelona, SpainDepartamento de Matemática Aplicada y Estadística, Universidad San Pablo CEU, 28668 Madrid, SpainIMMA, Instituto de Medicina Molecular Aplicada, Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, SpainServicio de Alergia, “Hospital Universitario de Gran Canaria, Dr. Negrin”, 35010 Las Palmas de G.C., SpainIMMA, Instituto de Medicina Molecular Aplicada, Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, SpainIMMA, Instituto de Medicina Molecular Aplicada, Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, SpainMetabolomics, understood as the science that manages the study of compounds from the metabolism, is an essential tool for deciphering metabolic changes in disease. The experiments rely on the use of high-throughput analytical techniques such as liquid chromatography coupled to mass spectrometry (LC-ToF MS). This hyphenation has brought positive aspects such as higher sensitivity, specificity and the extension of the metabolome coverage in a single run. The analysis of a high number of samples in a single batch is currently not always feasible due to technical and practical issues (i.e., a drop of the MS signal) which result in the MS stopping during the experiment obtaining more than a single sample batch. In this situation, careful data treatment is required to enable an accurate joint analysis of multi-batch data sets. This paper summarizes the analytical strategies in large-scale metabolomic experiments; special attention has been given to QC preparation troubleshooting and data treatment. Moreover, labeled internal standards analysis and their aim in data treatment, and data normalization procedures (intra- and inter-batch) are described. These concepts are exemplified using a cohort of 165 patients from a study in asthma.https://www.mdpi.com/2218-1989/9/11/247large-scalemetabolomicslc-qtof-msnormalizationasthma |
| spellingShingle | Juan Rodríguez-Coira María I Delgado-Dolset David Obeso Mariana Dolores-Hernández Guillermo Quintás Santiago Angulo Domingo Barber Teresa Carrillo María M. Escribese Alma Villaseñor Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts Metabolites large-scale metabolomics lc-qtof-ms normalization asthma |
| title | Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts |
| title_full | Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts |
| title_fullStr | Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts |
| title_full_unstemmed | Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts |
| title_short | Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts |
| title_sort | troubleshooting in large scale lc tof ms metabolomics analysis solving complex issues in big cohorts |
| topic | large-scale metabolomics lc-qtof-ms normalization asthma |
| url | https://www.mdpi.com/2218-1989/9/11/247 |
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