title: Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction.
abstract: BACKGROUND
  Mass spectrometric analysis of microbial metabolism provides a long list of possible compounds. Restricting the identification of the possible compounds to those produced by the specific organism would benefit the identification process. Currently, identification of mass spectrometry (MS) data is commonly done using empirically derived compound databases. Unfortunately, most databases contain relatively few compounds, leaving long lists of unidentified molecules. Incorporating genome-encoded metabolism enables MS output identification that may not be included in databases. Using an organism's genome as a database restricts metabolite identification to only those compounds that the organism can produce.
  
  
  RESULTS
  To address the challenge of metabolomic analysis from MS data, a web-based application to directly search genome-constructed metabolic databases was developed. The user query returns a genome-restricted list of possible compound identifications along with the putative metabolic pathways based on the name, formula, SMILES structure, and the compound mass as defined by the user. Multiple queries can be done simultaneously by submitting a text file created by the user or obtained from the MS analysis software. The user can also provide parameters specific to the experiment's MS analysis conditions, such as mass deviation, adducts, and detection mode during the query so as to provide additional levels of evidence to produce the tentative identification. The query results are provided as an HTML page and downloadable text file of possible compounds that are restricted to a specific genome. Hyperlinks provided in the HTML file connect the user to the curated metabolic databases housed in ProCyc, a Pathway Tools platform, as well as the KEGG Pathway database for visualization and metabolic pathway analysis.
  
  
  CONCLUSIONS
  Metabolome Searcher, a web-based tool, facilitates putative compound identification of MS output based on genome-restricted metabolic capability. This enables researchers to rapidly extend the possible identifications of large data sets for metabolites that are not in compound databases. Putative compound names with their associated metabolic pathways from metabolomics data sets are returned to the user for additional biological interpretation and visualization. This novel approach enables compound identification by restricting the possible masses to those encoded in the genome.
authors.affiliation: Center for Integrated BioSystems, Computer Science Department, Utah State University, Logan, 84322-8700, USA. bcweimer@ucdavis.edu.|Linda Crnic Institute for Down Syndrome, Department of Pediatrics, School of Medicine, University of Colorado Denver, 12700 E 19th Avenue, Aurora, CO, 80045, USA. bcweimer@ucdavis.edu.
authors.forename: A Ranjitha
authors.initials: AR
authors.lastname: Dhanasekaran
authors.affiliation: Center for Integrated BioSystems, Computer Science Department, Utah State University, Logan, 84322-8700, USA. bcweimer@ucdavis.edu.|Spillman Technologies, 4625 West Lake Park Blvd, Salt Lake City, UT, 84120, USA. bcweimer@ucdavis.edu.
authors.forename: Jon L
authors.initials: JL
authors.lastname: Pearson
authors.affiliation: Center for Integrated BioSystems, Computer Science Department, Utah State University, Logan, 84322-8700, USA. bcweimer@ucdavis.edu.|Western Dairy Center, Department of Nutrition, Dietetics, and Food Sciences, Utah State University, Logan, 84322-8700, USA. bcweimer@ucdavis.edu.
authors.forename: Balasubramanian
authors.initials: B
authors.lastname: Ganesan
authors.affiliation: University of California, Davis, School of Veterinary Medicine, 1089 Veterinary Medicine Dr., VM3B, Room 4023, Davis, CA, 95616, USA. bcweimer@ucdavis.edu.
authors.forename: Bart C
authors.initials: BC
authors.lastname: Weimer
mesh_terms: D001419:Bacteria / Q000145:classification / Q000378:metabolism*; D016208:Databases, Factual; D016680:Genome, Bacterial; D013058:Mass Spectrometry / Q000379:methods; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D012984:Software