Next Article in Journal
2-Deoxy-d-Glucose-Induced Metabolic Alteration in Human Oral Squamous SCC15 Cells: Involvement of N-Glycosylation of Axl and Met
Next Article in Special Issue
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
Previous Article in Journal
Untargeted Metabolomics Toward Systematic Characterization of Antioxidant Compounds in Betulaceae Family Plant Extracts
Previous Article in Special Issue
rMSIKeyIon: An Ion Filtering R Package for Untargeted Analysis of Metabolomic LDI-MS Images
Open AccessArticle

R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis

1
Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, J.Curie 14a, 50-383 Wrocław, Poland
2
Unidad Analítica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
3
Dell Pediatric Research Institute (DPRI), University of Texas at Austin, Austin, TX 78723, USA
4
Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78723, USA
5
Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, 50-366 Wrocław, Poland
6
Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, 46980 Valencia, Spain
*
Authors to whom correspondence should be addressed.
Metabolites 2019, 9(9), 187; https://doi.org/10.3390/metabo9090187
Received: 7 August 2019 / Revised: 28 August 2019 / Accepted: 12 September 2019 / Published: 17 September 2019
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 MS1 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 MS1 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 MS1 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. View Full-Text
Keywords: 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 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
Show Figures

Figure 1

MDPI and ACS Style

Peris-Díaz, M.D.; Sweeney, S.R.; Rodak, O.; Sentandreu, E.; Tiziani, S. R-MetaboList 2: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis. Metabolites 2019, 9, 187.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop