Metabolites 2013, 3(3), 787-819; doi:10.3390/metabo3030787
Technical Note

A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine

1,* email, 1email and 2,* email
Received: 10 July 2013; in revised form: 30 August 2013 / Accepted: 2 September 2013 / Published: 11 September 2013
(This article belongs to the Special Issue Analytical Techniques in Metabolomics)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract: Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC–LC), reversed-phase liquid chromatography (RP–LC), and gas chromatography (GC). All three techniques are coupled to a mass spectrometer (MS) in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM) and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow.
Keywords: untargeted metabolomics; pathway analysis; HILIC; RP; TOF; FT-ICR; Orbitrap; QTrap; mass spectrometer; cancer; human; plasma; urine
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MDPI and ACS Style

Zou, W.; She, J.; Tolstikov, V.V. A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine. Metabolites 2013, 3, 787-819.

AMA Style

Zou W, She J, Tolstikov VV. A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine. Metabolites. 2013; 3(3):787-819.

Chicago/Turabian Style

Zou, Wei; She, Jianwen; Tolstikov, Vladimir V. 2013. "A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine." Metabolites 3, no. 3: 787-819.

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