Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma

Metabolites, vol. 10, pp. 514

Abstract

A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91–113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis.

Authors 6

1. Tom van der Laan Aachen Analytical Biosciences and Metabolomics Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands

2. Isabelle Boom Aachen Analytical Biosciences and Metabolomics Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands

3. Joshua C. L. Maliepaard Aachen Analytical Biosciences and Metabolomics Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands

4. Anne-Charlotte Dubbelman Aachen Analytical Biosciences and Metabolomics Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands

5. Amy C. Harms Aachen Analytical Biosciences and Metabolomics Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands

6. Thomas Hankemeier corresponding Aachen Analytical Biosciences and Metabolomics Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands