In an effort to simplify and streamline compound identification from 
metabolomics data generated by liquid chromatography time-of-flight mass 
spectrometry, we have created software for constructing Personalized Metabolite 
Databases with content from over 15,000 compounds pulled from the public METLIN 
database (http://metlin.scripps.edu/). Moreover, we have added extra 
functionalities to the database that (a) permit the addition of user-defined 
retention times as an orthogonal searchable parameter to complement accurate 
mass data; and (b) allow interfacing to separate software, a Molecular Formula 
Generator (MFG), that facilitates reliable interpretation of any database 
matches from the accurate mass spectral data. To test the utility of this 
identification strategy, we added retention times to a subset of masses in this 
database, representing a mixture of 78 synthetic urine standards. The synthetic 
mixture was analyzed and screened against this METLIN urine database, resulting 
in 46 accurate mass and retention time matches. Human urine samples were 
subsequently analyzed under the same analytical conditions and screened against 
this database. A total of 1387 ions were detected in human urine; 16 of these 
ions matched both accurate mass and retention time parameters for the 78 urine 
standards in the database. Another 374 had only an accurate mass match to the 
database, with 163 of those masses also having the highest MFG score. 
Furthermore, MFG calculated a formula for a further 849 ions that had no match 
to the database. Taken together, these results suggest that the METLIN Personal 
Metabolite database and MFG software offer a robust strategy for confirming the 
formula of database matches. In the event of no database match, it also suggests 
possible formulas that may be helpful in interpreting the experimental results.