Dataset Information

Comparison of Full-Scan, Data-Dependent, and Data-Independent Acquisition Modes in Liquid Chromatography-Mass Spectrometry Based Untargeted Metabolomics

ABSTRACT: Full-scan, data-dependent acquisition (DDA), and data-independent acquisition (DIA) are the three common data acquisition modes in high resolution mass spectrometry-based untargeted metabolomics. It is an important yet underrated research topic on which acquisition mode is more suitable for a given untargeted metabolomics application. In this work, we compared the three data acquisition techniques using a standard mixture of 134 endogenous metabolites and a human urine sample. Both hydrophilic interaction and reversed-phase liquid chromatographic separation along with positive and negative ionization modes were tested. Both the standard mixture and urine samples generated consistent results. Full-scan mode is able to capture the largest number of metabolic features, followed by DIA and DDA (53.7% and 64.8% respective features fewer on average in urine than full-scan). Comparing the MS2 spectra in DIA and DDA, spectra quality is higher in DDA with average dot product score 83.1% higher than DIA in Urine(H), and the number of MS2 spectra (spectra quantity) is larger in DIA (on average 97.8% more than DDA in urine). Moreover, a comparison of relative standard deviation distribution between modes shows consistency in the quantitative precision, with the exception of DDA showing a minor disadvantage (on average 19.8% and 26.8% fewer features in urine with RSD < 5% than full-scan and DIA). In terms of data preprocessing convenience, full-scan and DDA data can be processed by well-established software. In contrast, several bioinformatic issues remain to be addressed in processing DIA data and the development of more effective computational programs is highly demanded.

INSTRUMENT(S): Liquid Chromatography MS - Reverse Phase (POS)” Liquid Chromatography MS - HILIC (NEG)”, Liquid Chromatography MS - HILIC (NEG), Liquid Chromatography MS - Reverse Phase (POS), Liquid Chromatography MS - Positive (LC-MS (Positive))

SUBMITTER: Jian Guo

PROVIDER: MTBLS1572 | MetaboLights | 2020-05-21

REPOSITORIES: MetaboLights

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Dataset's files

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			Action	DRS
	MTBLS1572	Other
	FILES	Other
	a_MTBLS1572_StdMixHigh_NEG_LC-MS.txt	Txt
	a_MTBLS1572_StdMixHigh_POS_LC-MS.txt	Txt
	a_MTBLS1572_StdMixLow_NEG_LC-MS.txt	Txt

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Publications

Comparison of Full-Scan, Data-Dependent, and Data-Independent Acquisition Modes in Liquid Chromatography-Mass Spectrometry Based Untargeted Metabolomics.

Guo Jian J Huan Tao T

Analytical chemistry 20200527 12

Full-scan, data-dependent acquisition (DDA), and data-independent acquisition (DIA) are the three common data acquisition modes in high resolution mass spectrometry-based untargeted metabolomics. It is an important yet underrated research topic on which acquisition mode is more suitable for a given untargeted metabolomics application. In this work, we compared the three data acquisition techniques using a standard mixture of 134 endogenous metabolites and a human urine sample. Both hydrophilic i ...[more]

PMID: 32401506

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