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Sample Set Information

Title RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database
Description The fragment pattern analysis of tandem mass spectrometry (MS/MS) has long been used for the structural characterization of metabolites. The construction of a plant-specific MS/MS data resource and database will enable complex phytochemical structures to be narrowed down to candidate structures. Therefore, a web-based database of MS/MS data pertaining to phytochemicals was developed and named ReSpect (RIKEN tandem mass spectral database). Of the 3595 metabolites in ReSpect, 76% were derived from 163 literature reports, whereas the rest was obtained from authentic standards. As a main web application of ReSpect, a fragment search was established based on only the m/z values of query data and records. The confidence levels of the annotations were managed using the MS/MS fragmentation association rule, which is an algorithm for discovering common fragmentations in MS/MS data. Using this data resource and database, a case study was conducted for the annotation of untargeted MS/MS data that were selected after quantitative trait locus analysis of the accessions (Gifu and Miyakojima) of a model legume Lotus japonicus. In the case study, unknown metabolites were successfully narrowed down to putative structures in the website.
Authors Yuji Sawada, Ryo Nakabayashi, Yutaka Yamada, Makoto Suzuki, Muneo Sato, Akane Sakata, Kenji Akiyama, Tetsuya Sakurai, Fumio Matsuda, Toshio Aoki, Masami Yokota Hirai, Kazuki Saito
Reference Sawada Y et al. (2012) Phytochemistry 82: 38-45

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The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Data Analysis Details Information

Title ReSpect
Description <MS/MS data in ReSpect>

The literature used for the MS/MS data were obtained from PubMed and Google Scholar, and the MS/MS data were manually digitalized. All literature used are listed in the information section in ReSpect ( For studies in which the relative intensity value of the MS fragment spectra was not described digitally, the heights of the MS peaks in the figures were manually measured and calculated. For literature data that have only m/z values without intensity data, the intensities of all ions to 100% were adjusted. In addition, the MS/MS data of the authentic standard compounds were acquired using Q-TOF/MS and QqQ/MS (Matsuda et al., 2010, 2009; Sawada et al., 2009a,b,c). All records used for ReSpect were categorized into compound classes according to the book (Cane, 1999; Kelly, 1999; Pinto, 1999; Sankawa,1999). The records were formatted using MassBank Record (Horai et al., 2010), which can accept MS/MS data as well as its metadata (summary, chemical, analytical, spectral and outer database links). As of September 2011, ReSpect contained 8649 records corresponding to 3595 metabolites. Specifically, the database contains 163 selected literature reports (3341 records corresponding to 2741 metabolites), Q-TOF/MS data (1050 records corresponding to 575 standard compounds) (Matsuda et al., 2010, 2009) and QqQ/MS data (4258 records corresponding to 861 standard compounds) (Sawada et al., 2009a,b,c). The ratios of the metabolite ontology classes are biased toward the available data and referenced classification of metabolites. In the data section of ReSpect, the example analyses (statistics and evaluation) were automatically executed based on the updated records.

<MS/MS fragment association rules in ReSpect>

In this study, association rules and index values (transaction, support, confidence, lift) of MS/MS data in the ReSpect records were enumerated using a module of Perl (Data Mining Association-Rules Version 0.10). To mimic the MS/MS data structure, the maximum value of the product ion and other product ions are defined as the antecedent and consequent, respectively, an antecedent is defined as a single ion, and the difference in m/z values between the antecedent and consequent is greater than 10. Moreover, a rare rule (only once in the transaction) was also excluded as invalid rules. On the basis of these definitions, the following invalid rules were excluded from the association rules: multiple antecedents in a rule, antecedent < consequent, and the estimated ion of the consequent corresponding to the isotopic ion of the antecedent. The index values of MS/MS fragmentation association rules with an antecedent (X), consequent (Y) and transaction (Z) are calculated as follows: support (X) = count (X)/count (Z), support (Y) = count (Y)/count (Z), support (X)Y) = count (X [ Y)/count (Z), confidence (X)Y) = count (X [ Y)/count (X), lift (X)Y) = confidence (X)Y)/support (Y). The MS/MS fragmentation association rules can be downloaded from the data section of ReSpect.

<Construction of web applications>

The web applications of ReSpect were implemented using HTML5.0, JavaScript, Perl, and MySQL and were hosted on CentOS. ReSpect has been successfully tested on Mozilla Firefox 3.6+, Safari 5.0+, Google Chrome 5.0+, Opera 10.0+, and Microsoft Internet Explorer 8.0+. The user can define the threshold for query and data resources with the following search options: polarity (positive, negative), spectra filters (similarity score, relative intensity, precursor ion and m/z tolerance), data type selection (ignores all single fragments and one major fragment spectrum) and data set selection (literature, Q-TOF/MS and QqQ/MS).


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