title: Increasing rigor in NMR-based metabolomics through validated and open source tools.
abstract: The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism's phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies.
authors.affiliation: Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA. Electronic address: heghbaln@wisc.edu.
authors.forename: Hamid R
authors.initials: HR
authors.lastname: Eghbalnia
authors.affiliation: Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
authors.forename: Pedro R
authors.initials: PR
authors.lastname: Romero
authors.affiliation: Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
authors.forename: William M
authors.initials: WM
authors.lastname: Westler
authors.affiliation: Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
authors.forename: Kumaran
authors.initials: K
authors.lastname: Baskaran
authors.affiliation: Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
authors.forename: Eldon L
authors.initials: EL
authors.lastname: Ulrich
authors.affiliation: Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
authors.forename: John L
authors.initials: JL
authors.lastname: Markley
mesh_terms: D000818:Animals; D016208:Databases, Factual; D006801:Humans; D008279:Magnetic Resonance Imaging; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D012984:Software; D049490:Systems Biology / Q000379:methods*