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Updated: Jan 25, 2026
Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
Published on: April 4, 2018
High-resolution MS/MS metabolomics by data-independent acquisition reveals urinary metabolic alteration in
Zhixiang Yan1,2, Ting Li1,2, Bin Wei1,2
1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
Introduction:
Traditional high-resolution MS1 based untargeted metabolomics suffers from low sensitivity, while low-resolution MS/MS based multiple reaction monitoring increases sensitivity at the cost of metabolite coverage and the mass accuracy.
Objectives:
To evaluate and apply the high-resolution MS/MS level untargeted metabolomics.
Methods:
SWATH based data-independent acquisition (DIA) was optimized to obtain MS/MS of all precursor ions.
Results:
SWATH-MS/MS could rescue MS1 obscured or saturated metabolites and potentially provide diagnostic fragments to differentiate isomers. For SWATH-MS/MS, 4944 out of 21492 (23.0%) and 2289 out of 12831 (17.8%) fragment ion features significantly changed (Fold change > 1.5, P < 0.05) between Normal and experimental acute ulcerative colitis (UC) groups in positive and negative ion mode, respectively. For SWATH-MS1, 1022 out of 4818 (21.2%) and 353 out of 2266 (15.6%) features significantly changed in positive and negative ion mode, respectively. By deciphering the metabolite profiles with high-resolution MS/MS, it allows versatile post-acquisition data mining such as open detection of different sub-metabolome. The method revealed a global urinary metabolic alteration and increased glucuronide and sulfate sub-metabolome in UC. The major limitation of untargeted SWATH-MS/MS is increased interferences derived from wider Q1 isolation window.
Conclusions:
SWATH-MS/MS is a versatile metabolomics strategy, merging the coverage of high-resolution untargeted metabolomics and the sensitivity of MS/MS.
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