SE133:/DS2
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.
Data Analysis Details Information
| ID | DS2 |
|---|---|
| Title | Data processing and analisys |
| Description | The raw data were recorded with the aid of MassLynx version 4.1 software (Waters). The raw chromatogram data were processed to produce a data matrix consisting of 1,589 metabolite signals (773 from positive and 816 from negative ion mode; Supplemental Data S1) using MetAlign (Lommen, 2009). The parameters used for data processing were as follows: maximum amplitude, 10,000; peak slope factor, 1; peak threshold factor, 6; average peak width at half weight, 8; scaling options, none; maximum shift per scan, 35; select min nr per peak set, 4. The data matrix generated by MetAlign was processed with in-house software written in Perl/Tk (Matsuda et al., 2009). By this procedure, the metabolite signals eluted before 0.85 min and after 12.0 min were discarded, original peak intensity values were divided with those of the internal standards (lidocaine: m/z = 235 [M + H]+, eluted at 4.19 min; camphor-10-sulfonic acid: m/z = 231 [M − H]−, eluted at 3.84 min, for the positive and negative ion modes, respectively) to normalize the peak intensity values, discarding low-intensity data (under signal-to-noise ratio < 5), and isotope peaks were removed by employing specific parameters (rthres > 0.8, ΔRt = 0.5 s, and Δm/z = 2 D). Metabolite signals were assigned unique accession codes, such as adn031026 (representing AtMetExpress Development negative ion mode data, peak number 31026). |
| Comment_of_details |
