Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data
The evaluation of liquid chromatography high-resolution mass spectrometry (LC-HRMS) raw data is a crucial step in untargeted metabolomics studies to minimize false positive findings. A variety of commercial or open source software solutions are available for such data processing. This study aims to...
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MDPI AG
2020-09-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/10/9/378 |
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| author | Selina Hemmer Sascha K. Manier Svenja Fischmann Folker Westphal Lea Wagmann Markus R. Meyer |
| author_facet | Selina Hemmer Sascha K. Manier Svenja Fischmann Folker Westphal Lea Wagmann Markus R. Meyer |
| author_sort | Selina Hemmer |
| collection | DOAJ |
| description | The evaluation of liquid chromatography high-resolution mass spectrometry (LC-HRMS) raw data is a crucial step in untargeted metabolomics studies to minimize false positive findings. A variety of commercial or open source software solutions are available for such data processing. This study aims to compare three different data processing workflows (Compound Discoverer 3.1, XCMS Online combined with MetaboAnalyst 4.0, and a manually programmed tool using R) to investigate LC-HRMS data of an untargeted metabolomics study. Simple but highly standardized datasets for evaluation were prepared by incubating pHLM (pooled human liver microsomes) with the synthetic cannabinoid A-CHMINACA. LC-HRMS analysis was performed using normal- and reversed-phase chromatography followed by full scan MS in positive and negative mode. MS/MS spectra of significant features were subsequently recorded in a separate run. The outcome of each workflow was evaluated by its number of significant features, peak shape quality, and the results of the multivariate statistics. Compound Discoverer as an all-in-one solution is characterized by its ease of use and seems, therefore, suitable for simple and small metabolomic studies. The two open source solutions allowed extensive customization but particularly, in the case of R, made advanced programming skills necessary. Nevertheless, both provided high flexibility and may be suitable for more complex studies and questions. |
| first_indexed | 2024-03-10T16:09:52Z |
| format | Article |
| id | doaj.art-a0a5654f96314fa98c6424294c47b2ac |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-10T16:09:52Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-a0a5654f96314fa98c6424294c47b2ac2023-11-20T14:33:47ZengMDPI AGMetabolites2218-19892020-09-0110937810.3390/metabo10090378Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics DataSelina Hemmer0Sascha K. Manier1Svenja Fischmann2Folker Westphal3Lea Wagmann4Markus R. Meyer5Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421 Homburg, GermanyDepartment of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421 Homburg, GermanyState Bureau of Criminal Investigation Schleswig-Holstein, 24116 Kiel, GermanyState Bureau of Criminal Investigation Schleswig-Holstein, 24116 Kiel, GermanyDepartment of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421 Homburg, GermanyDepartment of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421 Homburg, GermanyThe evaluation of liquid chromatography high-resolution mass spectrometry (LC-HRMS) raw data is a crucial step in untargeted metabolomics studies to minimize false positive findings. A variety of commercial or open source software solutions are available for such data processing. This study aims to compare three different data processing workflows (Compound Discoverer 3.1, XCMS Online combined with MetaboAnalyst 4.0, and a manually programmed tool using R) to investigate LC-HRMS data of an untargeted metabolomics study. Simple but highly standardized datasets for evaluation were prepared by incubating pHLM (pooled human liver microsomes) with the synthetic cannabinoid A-CHMINACA. LC-HRMS analysis was performed using normal- and reversed-phase chromatography followed by full scan MS in positive and negative mode. MS/MS spectra of significant features were subsequently recorded in a separate run. The outcome of each workflow was evaluated by its number of significant features, peak shape quality, and the results of the multivariate statistics. Compound Discoverer as an all-in-one solution is characterized by its ease of use and seems, therefore, suitable for simple and small metabolomic studies. The two open source solutions allowed extensive customization but particularly, in the case of R, made advanced programming skills necessary. Nevertheless, both provided high flexibility and may be suitable for more complex studies and questions.https://www.mdpi.com/2218-1989/10/9/378untargeted metabolomicsLC-HRMSdata processingfeature detectionA-CHMINACA |
| spellingShingle | Selina Hemmer Sascha K. Manier Svenja Fischmann Folker Westphal Lea Wagmann Markus R. Meyer Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data Metabolites untargeted metabolomics LC-HRMS data processing feature detection A-CHMINACA |
| title | Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data |
| title_full | Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data |
| title_fullStr | Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data |
| title_full_unstemmed | Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data |
| title_short | Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data |
| title_sort | comparison of three untargeted data processing workflows for evaluating lc hrms metabolomics data |
| topic | untargeted metabolomics LC-HRMS data processing feature detection A-CHMINACA |
| url | https://www.mdpi.com/2218-1989/10/9/378 |
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