SE133:/S1/M1
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.
Sample Information
| ID | S1 |
|---|---|
| Title | Arabidopsis thaliana |
| Organism - Scientific Name | Arabidopsis thaliana |
| Organism - ID | NCBI taxonomy 3702 |
| Compound - ID | |
| Compound - Source | |
| Preparation | Seedlings of Arabidopsis thaliana (Col-0) were grown in pots containing soil at 20°C with a 16 h daily photoperiod. Six weeks after germination, the 12th or 13th expanded rosette leaves (rosette leaf), the 1st and 2nd expanded cauline leaves (cauline leaf), the upper part of the inflorescence (inflorescence), and first internode tissues (stem) were collected from eight individual Arabidopsis plants at stage 6.3 (Boyes et al., 2001) and stored at −80°C until use. For metabolic phenotyping of Ds transposon insertion lines (Kuromori et al., 2004, 2006), 60lines of homozygous seeds were grown on the half‐strength MS medium plates at 20°C with a 16h daily photoperiod. Two weeks after germination, whole tissues of 20 seedlings were collected, weighed, and stored at −80°C. |
| Sample Preparation Details ID | |
| Comment | Matsuda et al (2009) Plant J 57: 555–577. |
Analytical Method Information
| ID | M1 |
|---|---|
| Title | LC-QTOF-MS |
| Method Details ID | MS1 |
| Sample Amount | 3 μL |
| Comment |
Analytical Method Details Information
| ID | MS1 |
|---|---|
| Title | LC-QTOF-MS Method |
| Instrument | Waters Acquity UPLC system; MS, Waters Q-Tof Premier |
| Instrument Type | UPLC-QTOF-MS |
| Ionization | ESI |
| Ion Mode | Positive |
| Description | The frozen tissues were homogenized in five volumes of 80% aqueous methanol containing 0.1% acetic acid, 0.5 mg/L of lidocaine, and d-camphor sulfonic acid (Tokyo Kasei) using a mixer mill (MM 300, Retsch) with a zirconia bead for 6 min at 20 Hz. Following centrifugation at 15,000g for 10 min and filtration (Ultrafree-MC filter, 0.2 μm, Millipore), the sample extracts were applied to an HLB μElution plate (Waters) equilibrated with 80% aqueous methanol containing 0.1% acetic acid. The eluates (3 μL) were subjected to metabolome analysis using LC-ESI-Q-TOF/MS.
Metabolome analysis was performed with an LC-ESI-Q-TOF/MS system equipped with an ESI interface (HPLC: Waters Acquity UPLC system; MS: Waters Q-TOF Premier) operated under previously described conditions (Matsuda et al., 2009). In the negative ion mode, the MS conditions were as follows: capillary voltage: +3.0 keV; cone voltage: 22.5 V; source temperature: 120°C; desolvation temperature: 450°C; cone gas flow: 50 L/h; desolvation gas flow: 800 L/h; collision energy: 2 V; detection mode: scan (m/z 100–2,000; dwell time: 0.45 s; interscan delay: 0.05 s, centroid); dynamic range enhancement mode: on. The scans were repeated for 19.5 min in a single run. |
| Comment_of_details | Matsuda et al. Plant Physiol.(2010) Feb;152(2):566-78 |
