title: Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.
abstract: Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups. Here we developed a bioinformatics workflow called MetaboDIA to build customized MS/MS spectral libraries using a user's own data dependent acquisition (DDA) data and to perform MS/MS-based quantification with DIA data, thus complementing conventional MS1-based quantification. MetaboDIA also allows users to build a spectral library directly from DIA data in studies of a large sample size. Using a marine algae data set, we show that quantification of fragment ions extracted with a customized MS/MS library can provide as reliable quantitative data as the direct quantification of precursor ions based on MS1 data. To test its applicability in complex samples, we applied MetaboDIA to a clinical serum metabolomics data set, where we built a DDA-based spectral library containing consensus spectra for 1829 compounds. We performed fragment ion quantification using DIA data using this library, yielding sensitive differential expression analysis.
authors.affiliation: Saw Swee Hock School of Public Health, National University of Singapore , Singapore, Singapore 117547.
authors.forename: Gengbo
authors.initials: G
authors.lastname: Chen
authors.affiliation: Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States.|Computational Biosciences Program, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States.
authors.forename: Scott
authors.initials: S
authors.lastname: Walmsley
authors.affiliation: Singapore National Eye Centre , Singapore 168751.|Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, National University of Singapore , Singapore 169857.
authors.forename: Gemmy C M
authors.initials: GCM
authors.lastname: Cheung
authors.affiliation: Singapore Eye Research Institute , Singapore 168756.
authors.forename: Liyan
authors.initials: L
authors.lastname: Chen
authors.affiliation: Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, National University of Singapore , Singapore 169857.|Singapore Eye Research Institute , Singapore 168756.|Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore 119228.
authors.forename: Ching-Yu
authors.initials: CY
authors.lastname: Cheng
authors.affiliation: Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, National University of Singapore , Singapore 169857.|Singapore Eye Research Institute , Singapore 168756.|Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore 119228.|Neuroscience and Behavioural Disorders Programme, Duke-NUS Medical School, National University of Singapore , Singapore 169857.
authors.forename: Roger W
authors.initials: RW
authors.lastname: Beuerman
authors.affiliation: Singapore National Eye Centre , Singapore 168751.|Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, National University of Singapore , Singapore 169857.|Singapore Eye Research Institute , Singapore 168756.|Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore 119228.
authors.forename: Tien Yin
authors.initials: TY
authors.lastname: Wong
authors.affiliation: Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, National University of Singapore , Singapore 169857.|Singapore Eye Research Institute , Singapore 168756.|Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore 119228.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhou
authors.affiliation: Saw Swee Hock School of Public Health, National University of Singapore , Singapore, Singapore 117547.|Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research , Singapore, Singapore 138632.
authors.forename: Hyungwon
authors.identifier: 0000-0002-6687-3088
authors.initials: H
authors.lastname: Choi
mesh_terms: D000368:Aged; D000460:Chlorophyta / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D062126:Databases, Chemical / Q000706:statistics & numerical data; D005260:Female; D006801:Humans; D008297:Male; D055442:Metabolome; D055432:Metabolomics / Q000379:methods* / Q000706:statistics & numerical data; D053719:Tandem Mass Spectrometry / Q000379:methods*; D057188:Workflow