R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis
Technological advancements have permitted the development of innovative multiplexing strategies for data independent acquisition (DIA) mass spectrometry (MS). Software solutions and extensive compound libraries facilitate the efficient analysis of MS<sup>1</sup> data, regardless of the a...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-09-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/9/9/187 |
| _version_ | 1818296434120720384 |
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| author | Manuel D. Peris-Díaz Shannon R. Sweeney Olga Rodak Enrique Sentandreu Stefano Tiziani |
| author_facet | Manuel D. Peris-Díaz Shannon R. Sweeney Olga Rodak Enrique Sentandreu Stefano Tiziani |
| author_sort | Manuel D. Peris-Díaz |
| collection | DOAJ |
| description | Technological advancements have permitted the development of innovative multiplexing strategies for data independent acquisition (DIA) mass spectrometry (MS). Software solutions and extensive compound libraries facilitate the efficient analysis of MS<sup>1</sup> data, regardless of the analytical platform. However, the development of comparable tools for DIA data analysis has significantly lagged. This research introduces an update to the former MetaboList R package and a workflow for full-scan MS<sup>1</sup> and MS/MS DIA processing of metabolomic data from multiplexed liquid chromatography high-resolution mass spectrometry (LC-HRMS) experiments. When compared to the former version, new functions have been added to address isolated MS<sup>1</sup> and MS/MS workflows, processing of MS/MS data from stepped collision energies, performance scoring of metabolite annotations, and batch job analysis were incorporated into the update. The flexibility and efficiency of this strategy were assessed through the study of the metabolite profiles of human urine, leukemia cell culture, and medium samples analyzed by either liquid chromatography quadrupole time-of-flight (q-TOF) or quadrupole orbital (q-Orbitrap) instruments. This open-source alternative was designed to promote global metabolomic strategies based on recursive retrospective research of multiplexed DIA analysis. |
| first_indexed | 2024-12-13T04:03:28Z |
| format | Article |
| id | doaj.art-c792415461d844e98b3297dda1b165f4 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-12-13T04:03:28Z |
| publishDate | 2019-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-c792415461d844e98b3297dda1b165f42022-12-22T00:00:22ZengMDPI AGMetabolites2218-19892019-09-019918710.3390/metabo9090187metabo9090187R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry AnalysisManuel D. Peris-Díaz0Shannon R. Sweeney1Olga Rodak2Enrique Sentandreu3Stefano Tiziani4Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, J.Curie 14a, 50-383 Wrocław, PolandDell Pediatric Research Institute (DPRI), University of Texas at Austin, Austin, TX 78723, USADepartment of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, 50-366 Wrocław, PolandUnidad Analítica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, SpainDell Pediatric Research Institute (DPRI), University of Texas at Austin, Austin, TX 78723, USATechnological advancements have permitted the development of innovative multiplexing strategies for data independent acquisition (DIA) mass spectrometry (MS). Software solutions and extensive compound libraries facilitate the efficient analysis of MS<sup>1</sup> data, regardless of the analytical platform. However, the development of comparable tools for DIA data analysis has significantly lagged. This research introduces an update to the former MetaboList R package and a workflow for full-scan MS<sup>1</sup> and MS/MS DIA processing of metabolomic data from multiplexed liquid chromatography high-resolution mass spectrometry (LC-HRMS) experiments. When compared to the former version, new functions have been added to address isolated MS<sup>1</sup> and MS/MS workflows, processing of MS/MS data from stepped collision energies, performance scoring of metabolite annotations, and batch job analysis were incorporated into the update. The flexibility and efficiency of this strategy were assessed through the study of the metabolite profiles of human urine, leukemia cell culture, and medium samples analyzed by either liquid chromatography quadrupole time-of-flight (q-TOF) or quadrupole orbital (q-Orbitrap) instruments. This open-source alternative was designed to promote global metabolomic strategies based on recursive retrospective research of multiplexed DIA analysis.https://www.mdpi.com/2218-1989/9/9/187liquid chromatography high-resolution mass spectrometrydata-independent acquisitionall ion fragmentationtargeted analysisuntargeted analysismetabolomicsR programmingfull-scan MS/MS processingR-MetaboList 2 |
| spellingShingle | Manuel D. Peris-Díaz Shannon R. Sweeney Olga Rodak Enrique Sentandreu Stefano Tiziani R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis Metabolites liquid chromatography high-resolution mass spectrometry data-independent acquisition all ion fragmentation targeted analysis untargeted analysis metabolomics R programming full-scan MS/MS processing R-MetaboList 2 |
| title | R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis |
| title_full | R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis |
| title_fullStr | R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis |
| title_full_unstemmed | R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis |
| title_short | R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis |
| title_sort | r metabolist 2 a flexible tool for metabolite annotation from high resolution data independent acquisition mass spectrometry analysis |
| topic | liquid chromatography high-resolution mass spectrometry data-independent acquisition all ion fragmentation targeted analysis untargeted analysis metabolomics R programming full-scan MS/MS processing R-MetaboList 2 |
| url | https://www.mdpi.com/2218-1989/9/9/187 |
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