SE133:/MS2
From Metabolonote
Sample Set Information
| ID | TSE7 |
|---|---|
| Title | Regular expressions of MS/MS spectra for partial annotation of metabolite features |
| Description | Partial annotation and characterization of metabolite structures on the basis of data from tandem mass spectrometry (MS/MS) spectra are technical bottlenecks in metabolomics. Novel approaches should be explored for evaluation of spectral similarities among structurally related compounds as well as for description of fragmentation motifs commonly observed in MS/MS spectra. |
| Authors | Fumio Matsuda |
| Reference | Matsuda (2016) Metabolomics, July, 12:113 |
| Comment | MS/MS strings of MassBank dataset and MS/MS strings of Arabidopsis (ATH) and rice (OSA) MS/MS spectra data are stored in DROP Met as "Test dataset for the regular expression of MS/MS spectra data" |
The raw data files are available at DROP Met web site in PRIMe database of RIKEN.
Analytical Method Details Information
| ID | MS2 |
|---|---|
| Title | LC-QTOF-MS/MS Method (rice) |
| Instrument | LC, Waters Acquity UPLC system; Q-TOF-MS, Waters Q-Tof Premier |
| Instrument Type | UPLC-QTOF-MS |
| Ionization | ESI |
| Ion Mode | Positive |
| Description | Sample metabolomic data were acquired using four time-of-flight mass spectrometers (TOF-MS), including CE-TOF-MS for analysis of polar metabolites, GC-TOF-MS for analysis of primary metabolites, LC-Q-TOF-MS for analysis of secondary metabolites and LC-IT-TOF-MS for analysis of lipids. Analysis was performed in triplicate, and the samples were extracted from each pipeline using optimized methods. For the LC-Q-TOF -MS pipeline, 100 mg of rice seed powder was homogenized in 10 volumes of 5% aqueous methanol containing 0.1% acetic acid (Tokyo Kasei, http://www.tciamerica.com/) using an MM300 mixer mill (Retsch, http://www.retsch.com/) with a zirconia bead for 10 min at 20 Hz. Next, the samples were centrifuged at 15000 g for 10 min. The supernatant (500 ll) was diluted to 5.0 ml using water containing 0.1% acetic acid, and was applied to a 3 cc OASIS HLB cartridge (Waters, http://www .waters.com/) that had been equilibrated with 0.5% aqueous methanol containing 0.1% acetic acid. After pre-equilibrium with 5 ml of 0.5% aqueous methanol containing 0.1% acetic acid, metabolites were eluted with 3 ml of 90% aqueous methanol containing 0.1% acetic acid. The eluate was dried under vacuum and then suspended in 100 ll water containing the internal standard (0.5 mg/ml lidocaine). Insoluble residue was removed by filtration using an Ultrafree-MC filter with 0.2 lm pore size (Millipore, http://www.millipore.com/). The samples (3µl) were subsequently subjected to metabolome analysis by liquid chromatography coupled with electrospray quadrupole time-of-flight tandem mass spectrometry (LC-ESI-Q-TOF-MS) using an Acquity BEH ODS column (LC, Waters Acquity UPLC system; Q-TOF-MS, Waters Q-Tof Premier). |
| Comment_of_details |
