ExactMassDB Searching

About the Database

ExactMassDB stores all the possible elemental compositions with the kinds and maximum numbers of atoms (shown below) that satisfy the Senor and the Lewis valence rules.

Last updated.




Atom maximum number
C 100
H 200
O 50
N 10
P 10
S 10

Our previous survey demonstrated that 95.65% of the compounds in the Dictionary of Natural Products , 186,788 compounds in the range 50-1500 Da) consist of C, H, O, N, P and S within the ranges C: 1-95, H: 1-182, N: 0-10, O: 1-45, P: 0-6 and S: 0-5 (Iijima et al., 2008). Thus we chose the atom kinds and numbers listed above for construction of ExactMassDB. It was estimated that 99.5% of the compounds consisting of C, H, O, N, P and S in KEGG and 99.1% in KNApSAcK were within the criteria. The database would cover most of the natural compounds.

以前調査した結果では、Dictionary of Natural Productsに含まれるC, H, O, N, P, Sで構成される化合物(186,788化合物、50-1500 Da)のうち、95.65%が、C: 1-95, H: 1-182, N: 0-10, O: 1-45, P: 0-6, S: 0-5の範囲で構成されることが分かりました(Iijima et al., 2008)。そこで、ExactMassDBデータベースの構築には、これよりも広い原子数設定をしました(上記)。この原子数の範囲は、C, H, O, N, P, Sから構成されるKEGG登録化合物の99.5%、 KNApSAcK登録化合物の99.1%をカバーしていたので、ExactMassDB-HR2は、ほとんどの天然物の組成式を網羅していると考えられます。

Search Limit: 100

The maximum record number that returns for a single query is 100 as default. The number can be set to a smaller one by setting the "limit" parameter.

When the number of search results exceeds the maximum number, the value of "is-limited" will be set to "true". It means that not all of the search results were written in the returned text, so please be careful to discuss about the results.

The "is-limited" value is written in the returned text when the "output" parameter has been set to "txth" or "xml".




Output Example

Here is a part of results when "txth" is selected for the "output" parameter.



Search Test

# db-name molecular-formula dbe formula-weight id description
ExactMassDB C16H11O2N10P3S1 21.0 500.0000046695
ExactMassDB C32H1N6P1       37.0 500.0000320763
ExactMassDB C6H37O5P9S1      2.0 500.0000372918
ExactMassDB C19H17O10P1S2   13.0 500.0000767653
ExactMassDB C1H12O19N10S1    1.0 500.0000892805
ExactMassDB C7H31O3N4P7S2    5.0 500.0000988854
ExactMassDB C4H21O10N8P1S4   0.0 500.0001109521
ExactMassDB C23H21O1P5S1    21.0 500.0001262922
db-name ExactMassDB
id blank
description blank


Not planned.




The elemental compositions and their exact mass values registered in the ExactMassDB.

ex.tar.gz.aa (1.00 GB)
ex.tar.gz.ab (1.00 GB)
ex.tar.gz.ac (1.00 GB)
ex.tar.gz.ad (886 MB)

Download the four files above, and concatenate them with cat command below.

$ cat ex.tar.gz.* > ex.tar.gz

Then untar with tar command.

$ tar zxf ex.tar.gz
$ tar zxf ExactMassDB.tar.gz

# records: 417,844,582
File size: ExactMassDB.txt 15.6 GB (after decompression)

The java software used to create the data shown above.

CreateExactMassDB_1.0.zip (7 KB)



ex.tar.gz.aa (1.00 GB)
ex.tar.gz.ab (1.00 GB)
ex.tar.gz.ac (1.00 GB)
ex.tar.gz.ad (886 MB)


$ cat ex.tar.gz.* > ex.tar.gz


$ tar zxf ex.tar.gz
$ tar zxf ExactMassDB.tar.gz

組成式数: 417,844,582
展開後サイズ: ExactMassDB.txt 15.6 GB


CreateExactMassDB_1.0.zip (7 KB)


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