10.2.0.1 enterprise edition

The informatics system consisted of four major components, the Laboratory Information Management System (LIMS), the data extraction and peak-identification software, data processing tools for QC and compound identification, and a collection of information interpretation and visualization tools for use by data analysts^{32 (link)}. The hardware and software foundations for these informatics components were the LAN backbone, and a database server running Oracle 10.2.0.1 Enterprise Edition.

Bioinformatics: The informatics system consisted of four major components, the Laboratory Information Management System (LIMS), the data extraction and peak-identification software, data processing tools for QC and compound identification, and a collection of information interpretation and visualization tools for use by data analysts. The hardware and software foundations for these informatics components were the LAN backbone, and a database server running Oracle 10.2.0.1 Enterprise Edition.

Raw data was extracted, peak-identified, and QC processed using a LAN backbone and a database server running Oracle 10.2.0.1 Enterprise Edition. These systems are built on a web-service platform utilizing Microsoft’s .NET technologies. Compounds were identified by comparison to a library of purified standards or recurring unknown entities; this library is maintained by Metabolon and contains the retention time/index (RI), mass to charge ratio (m/z), and chromatographic data (including MS/MS spectral data). Biochemical identifications are based on three criteria: retention index within a narrow RI window, accurate mass match to the library ± 10 ppm, and the MS/MS forward and reverse scores between the experimental data and authentic standards. These MS/MS scores are based on a comparison of ions present in the experimental spectrum to ions present in the library spectrum. More than 3300 commercially available purified standard compounds have been acquired and registered into Metabolon’s Laboratory Information Management System (LIMS) for analysis on all platforms. Additional mass spectral entries have been made for structurally unnamed biochemicals, identified due to their recurrent nature.

Global biochemical profiles were determined by using the serum (12 mice/group) from each mouse. Metabolomic profiling analysis was performed by Metabolon (Durham, NC, USA) using ultra-high-performance liquid chromatography–tandem mass spectroscopy (UPLC-MS/MS) platforms, as previously described (15 (link)). In brief, sample (100 µl serum) preparation was conducted by using a proprietary series of organic and aqueous extractions to remove the protein fraction while allowing maximum recovery of small molecules. The resultant extract was divided into 4 fractions: one for analysis by UPLC-MS/MS (positive mode), one for UPLC-MS/MS (negative mode), one for GC-MS, and one for backup. The sample extract was dried and then reconstituted in acidic or basic liquid chromatography–compatible solvents, each of which contained ≥8 injection standards at fixed concentrations to ensure injection and chromatographic consistency. The data were extracted, with peaks and compounds identified by using the local area network backbone and database server running Oracle 10.2.0.1 Enterprise Edition (Oracle, Redwood City, CA, USA).

The informatics system consisted of four major components, the LIMS, data extraction and peak-identification software, data processing tools for QC and compound identification, and a collection of information interpretation and visualization tools for use by data analysts. The hardware and software foundations for these informatics components were the LAN backbone and a database server running Oracle 10.2.0.1 Enterprise Edition.

The informatics system consists of four major components, the Laboratory Information Management System (LIMS, see Supplementary Information), the data extraction and peak-identification software, data processing tools for QC and compound identification, and a collection of statistical, visualization, and interpretation tools for use by data analysts. The hardware and software foundations for these informatics components are the LAN backbone and database servers running Oracle 10.2.0.1 Enterprise Edition.