The Kazusa Metabolomics Portal



Welcome to MatchedIonsFinder's site!

Our computational tool, MatchedIonsFinder is designed to revise an alignment matrix of metabolites which was generated from multiple data sets of ions detected by liquid chromatography mass-spectrometry


Several software programs that facilitate processing of data from multiple spectrograms obtained by liquid chromatography-mass spectrometry are available. Generally, most alignments within a given matrix are correct, but some alignments seem incorrect, and incorrect alignments must be revised manually. Thus, we developed a software tool, MatchedIonsFinder, that revises alignments using a defined algorithm.

Detail of the tool MatchedIonsFinder is published in Plant Biotechnology (Vol.29 No.1, 2012).


  • MatchedIonsFinder (ver 1.1)

  • MatchedIonsFinder_MSMS (ver 1.3.2)
    If information of mass fragmentation patterns is available to the aligned matrix, this program is suitable for alignment revision. To run this program, The MS fragmentation file set (see below) is necessary.

    - Updated [2012/08/21]
    A default parameter setting ($MSdif) is changed and a misstype of function name is fixed. Codes and comments are orverall refactored in ver.1.3.2
    - [2012/04/09]
    Division by zero errors have occurred when MSMS data that have only one fragment were processed for correlation coefficient calculations. The bug is fixed in ver.1.3

  • The aligned matrix of tomato samples from IonMatch
    Here we provide an example of an aligned matrix of tomato metabolites as a tab-deliminated text file, which can be used directly for the MatchedIonsFinder calculation. Tomato fruits of three cultivars, Lovely-Ai, House-Momotaro and Furikoma were analyzed by liquid chromatography-Fourier transform ion cyclotron resonance-MS (LC-FT/ICR-MS) as described by Iijima et al. (Plant J. 54: 949-62, 2008), and analyzed using the program PowerFT for ion feature detection. Triplicate analyses were carried out for the three cultivars. The file names, "sly3-01", "sly3-02" and "sly3-03" are for the data sets for Lovely-Ai, "sly3-04", "sly3-05" and "sly3-06" for House-Momotaro, and "sly3-07", "sly3-08" and "sly3-09" for Furikoma. The ion features from each sample were aligned by IonMatch tool.

  • The MS fragmentation file set for MatchedIonsFinder_MSMS
    Here we provide an example of a file set of tomato metabolites for MatchedIonsFinder_MSMS, in which information of mass fragmentation patterns is used for revision of an aligned matrix. The file set contains two folders, "peakGroups" , which have files for the relationship between ion peak identifiers (PeakIDs) and MS/MS spectrum identifiers, and "ms2DataUsed", which have files for information of MS/MS spectrums and spectrum patters. The two folders in the site contain files for nine tomato spectrums of the cultivars, Lovely-Ai, House-Momotaro and Furikoma. These folders should be located in the same directory of the program MatchedIonsFinder or MatchedIonsFinder_MSMS.

  • Results of revision by MatchedIonsFinder and MatchedIonsFinder_MSMS
    Here we provide the results of revision of alignment matrices of tomato metabolites by MatchedIonsFinder and MatchedIonsFinder_MSMS. 

    For the revised matrix by MatchedIonsFinder, click here

    For the revised matrix by MatchedIonsFinder_MSMS, click here.


Use the following permanent URL to link to MatchedIonsFinder. Don't use the URL of this web page. It may change.