Targeted LC/MS/MS Metabolomics Protocol

A robust targeted LC/MS/MS method has recently been developed and used in a number of studies in the Northwest Metabolomics Research Center (NW-MRC).^{11 (link),15 (link),53 (link),62 (link)–67 (link)} In this study, the MS data from the same samples as those measured by NMR, collected in our previous study,^{15 (link)} were used to demonstrate the performance of the NMR–MS combination. Briefly, the LC/MS/MS experiments were performed on an Agilent 1260 LC (Agilent Technologies, Santa Clara, CA) AB Sciex QTrap 5500 MS (AB Sciex, Toronto, ON) system. Table S2 shows the LC gradient conditions. We monitored 99 and 59 MRM transitions in negative and positive mode, respectively (158 transitions in total). The optimized MS conditions are listed in Table S3. The extracted MRM peaks were integrated using MultiQuant version 2.1 (AB Sciex). The LC/MS/MS data were also deposited into the DRCC (Study ST000284).⁶¹

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Deng L., Gu H., Zhu J., Nagana Gowda G.A., Djukovic D., Chiorean E.G, & Raftery D. (2016). Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls. Analytical chemistry, 88(16), 7975-7983.

Publication 2016

Agilent 1260 LC MultiQuant version 2.1

Ms ms

Corresponding Organization :

Other organizations : East China University of Technology, University of Washington, Indiana University Health, Indiana University – Purdue University Indianapolis, Fred Hutch Cancer Center, North Seattle College, Purdue University West Lafayette

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Variable analysis

independent variables

LC gradient conditions

dependent variables

MRM transitions in negative and positive mode
Extracted MRM peaks

control variables

Not explicitly mentioned

controls

Positive controls: Not specified
Negative controls: Not specified

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