MassBase 1.0
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MassBase: A mass spectral tag archive for metabolomics.
The MassBase database is fundamental for metabolomics, which provides raw mass chromatograms from various biological samples and text-file data processed from the raw chromatograms. You can view the raw or processed chromatograms of your interest and also download the files of interest or even in bulk all datasets. We expect not only that biologists use the full function of the database to understand metabolisms in the organisms of interest with help of other databases such as MassBank and KNApSAcK, but also that bioinformatics researchers fully use the wealth of the information of mass chromatograms to develop pipeline software for extracting metabolite peaks and annotating metabolites, which is crucial to accelerate metabolomics approaches to link DNA information to metabolisms.
Since 2002 our laboratory has been working on metabolome analysis of various organisms by using nine state-of-the-art mass spectrometers, and accumulated mass chromatograms of various biological samples in our server, with an intention of archiving the metabolome data for public use. A distress of such archiving metabolite data is that extracting metabolite information from the raw mass chromatograms by the present software is still immature to represent the whole metabolites correctly, and therefore large-scaled metabolome databases that provide information of annotated metabolites is scare. It is quite contrast to the situation of base calling for nucleotide sequence from a capillary chromatogram by the Phred program. Thus, we decided to provide the raw mass chromatograms and text-file formats converted from the raw data to the public through the MassBase, by which bioinformaticians can easily access the wealth of the information to develop software. The database is also useful to individual biologists who wish to search mass chromatograms to find metabolites of interest or compare them with their mass chromatograms to understand the profile differences between their biological samples.
We thank the Kazusa DNA Research Institute Foundation and the New Energy and industrial Technology Development Organization for their supports.

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