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 MS1 data, regardless of the analytical platform. How...

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Bibliographic Details
Published inMetabolites Vol. 9; no. 9; p. 187
Main Authors Peris-Díaz, Manuel D., Sweeney, Shannon R., Rodak, Olga, Sentandreu, Enrique, Tiziani, Stefano
Format Journal Article
LanguageEnglish
Published Basel MDPI AG 17.09.2019
MDPI
Subjects
all ion fragmentation
Annotations
Asymmetry
Automation
Cell culture
Data processing
data-independent acquisition
full-scan MS/MS processing
Liquid chromatography
liquid chromatography high-resolution mass spectrometry
Mass spectrometry
Mass spectroscopy
Metabolites
Metabolomics
Qualitative research
R programming
R-MetaboList 2
Scientific imaging
Sensors
targeted analysis
untargeted analysis
Urine
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Summary: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.
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ISSN:2218-1989
2218-1989
DOI:10.3390/metabo9090187