MetaboMSDIA: A tool for implementing data-independent acquisition in metabolomic-based mass spectrometry analysis

Carlos Augusto Ledesma-Escobar; Feliciano Priego-Capote; Mónica Calderón-Santiago

doi:10.1016/j.aca.2023.341308

MetaboMSDIA: A tool for implementing data-independent acquisition in metabolomic-based mass spectrometry analysis

Anal Chim Acta. 2023 Jul 25:1266:341308. doi: 10.1016/j.aca.2023.341308. Epub 2023 May 12.

Authors

Carlos Augusto Ledesma-Escobar¹, Feliciano Priego-Capote², Mónica Calderón-Santiago³

Affiliations

¹ Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Nanochemistry University Institute (IUNAN), Campus of Rabanales, University of Córdoba, Córdoba, Spain.
² Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Nanochemistry University Institute (IUNAN), Campus of Rabanales, University of Córdoba, Córdoba, Spain; CIBER Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Spain. Electronic address: feliciano.priego@uco.es.
³ Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Nanochemistry University Institute (IUNAN), Campus of Rabanales, University of Córdoba, Córdoba, Spain. Electronic address: b42casam@uco.es.

PMID: 37244659
DOI: 10.1016/j.aca.2023.341308

Abstract

Data-dependent acquisition (DDA) is the most widely used mode in untargeted metabolomic analysis despite its limited tandem mass spectrometry (MS2) detection coverage. We present MetaboMSDIA for complete processing of data-independent acquisition (DIA) files by the extraction of multiplexed MS2 spectra and further identification of metabolites in open libraries. In the analysis of polar extracts from lemon and olive fruits, DIA allows one to obtain multiplexed MS2 spectra for 100% of precursor ions compared to 64% of precursor ions from average MS2 acquisition in DDA. MetaboMSDIA is compatible with MS2 repositories and homemade libraries prepared by analysis of standards. An additional option is based on filtering molecular entities by searching for selective fragmentation patterns according to selective neutral losses or product ions to target the annotation of families of metabolites. Combining both options, the applicability of MetaboMSDIA was tested by annotating 50 and 35 metabolites in polar extracts from lemon and olive fruit, respectively. MetaboMSDIA is particularly proposed to increase the acquisition coverage in untargeted metabolomics and to improve spectral quality, which are two critical pillars for the tentative annotation of metabolites. The R script used in MetaboMSDIA workflow is available at github repository (https://github.com/MonicaCalSan/MetaboMSDIA).

Keywords: Data-independent acquisition; Mass spectrometry; Multiplexed MS2 spectra; R package; metabolites annotation.

MeSH terms

Ions
Metabolomics* / methods
Plant Extracts
Tandem Mass Spectrometry* / methods
Workflow

Substances

Ions
Plant Extracts