Metabolomics

Dataset Information

347

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.

Serum metabolome of 40 age-related macular degeneration patients and 20 control samples was analyzed using untargeted mass spectrometry. We used data dependent acquisition data to build a MS/MS spectral assay library for more than 1,000 compounds and performed targeted extraction of MS2 ion chromatograms from data independent acquisition analysis.

INSTRUMENT(S): TripleTOF 5600 (AB Sciex)

SUBMITTER: Hyungwon Choi  

PROVIDER: MTBLS417 | MetaboLights | 2018-03-26

REPOSITORIES: MetaboLights

altmetric image

Publications

Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.

Chen Gengbo G   Walmsley Scott S   Cheung Gemmy C M GCM   Chen Liyan L   Cheng Ching-Yu CY   Beuerman Roger W RW   Wong Tien Yin TY   Zhou Lei L   Choi Hyungwon H  

Analytical chemistry 20170418 9


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 pre  ...[more]

Publication: 1/3

Similar Datasets

2017-07-04 | PXD006190 | Pride
2019-01-07 | PXD012219 | Pride
2017-11-20 | PXD006934 | Pride
2018-09-17 | PXD009624 | Pride
2019-02-14 | PXD009623 | Pride
2014-06-09 | PXD000186 | Pride
2016-07-14 | PXD004188 | Pride
2014-08-04 | PXD000154 | Pride
2018-12-18 | PXD010876 | Pride
2018-12-18 | PXD010869 | Pride