The Kazusa Metabolomics Portal



MassChroViewer is a data viewer for liquid chromatography (LC)–mass spectrometry (MS) data. LC-MS data in mzXML or mzML format are visualized in two-dimensions by retention time (RT) vs. m/z and the peak positions extracted using data processing software can be overlaid. A mass ruler function to evaluate mass accuracy and adduct assignment, immediate colour strength change to view peaks in wide intensity range and MS/MS visualization tool will help assess the quality of raw and processed data. A database search tool linked to a mass substructure calculator is used to metabolite annotations.



Link to this page

Use the URL below to cite the MassChroViewer website.
OK: http://www.kazusa.or.jp/komics/software/MassChroViewer

Don't use the URL written in the address bar of your browser. The URL might be changed in future.
NG: http://www.kazusa.or.jp/komics/en/tool-en/222-masschroviewer.html

Computer requirements:

A PC (64 bit, > 4GB RAM is recommended) with Java Runtime Environment (JRE 64 bit, version 1.7 or later) is required to run MassChroViewer. See Oracle's website for installation of Java.

We tested the tool using following PCs:
Windows10, MacOSX 10.9.5 and CentOS7.2 Linux


MassChroViewer_1.9.0.zip (zip compressed: 27.5 MB, Updated on 2 December 2021)


MassChroViewer_manual_en.pdf (English 2.5 MB)

MassChroViewer_manual_ja.pdf (Japanese 2.7 MB)

Sample Data:

Sample of raw chromatogram data and a peak table file is available. Details of the sample metadata are available at Metabolonote. The binary raw data is available at MassBase.

NameDescriptionMetabolonote IDMassBase IDDownload
S1_Cont_HRes_DX_ms2.zip Parsley shoot analyzed by LC-FT-ICR-MS in ESI positive mode at a high resolution (100,000), with dynamic exclusion setting to obtain MS2 SE61_S21_M011 MDLC1_48041 Download (35.4 MB)
S2_Cont_LRes_DX_ms2-3.zip Parsley shoot analyzed by LC-FT-ICR-MS in ESI positive mode at a low-resolution (12,500), with dynamic exclusion setting to obtain MS2 and MS3 SE61_S21_M015 MDLC1_47225 Download (16.0 MB)
S3_15N_HRes_noDX_ms2.zip 15N labeled parsley shoot analyzed by LC-FT-ICR-MS in ESI positive mode at a high-resolution (100,000) without dynamic exclusion setting to obtain MS2 SE61_S22_M014 MDLC1_48043 Download (37.4 MB)
S4_mock_HRes_DX_ms2.zip Mock control analyzed by the same procedure as S1_Cont_HRes_DX_ms2 without parsley sample. SE61_S02_M01 MDLC1_47219 Download (25.3 MB)
S1_peakLists.zip A set of peaks extracted from the sample S1_Cont_HRes_DX_ms2 using PowerGet software is saved in three different text format that can be imported by MassChroViewer. SE61_S21_M011_D1   Download (1.02 MB)

JChemPaintMs.jar Library:

The library JChemPaintMs.jar for the Fragment Calculator function is an open source software licensed under the GNU Lesser General Public License, Version 2.1. The source codes of the JChemPaint (available at http://svn.code.sf.net/p/cdk/svn/jchempaint/, revision 15623) is used in the library with a slight modification. The source code of JChemPaintMs.jar is included in the jar file.

JChemPaintMs_0.2.1.zip (zip compressed: 18.7 MB)

flavonoidsearch.jar Library:

The library flavonoid.jar for the FlavonoidSearch GUI tool is an open source software licensed under the GNU Lesser General Public License, Version 2.1.


Sakurai N and Shibata (2017) Tools and databases for an integrated metabolite annotation environment for liquid chromatography–mass spectrometry–based untargeted metabolomics. Carotenoid Science 22: 16-22


MassChroViewer is available free of charge for academic purpose.


Version Info.:

2 December 2021
- The Close All item was added in the File menu.
- The memory releasing after closing the data was improved.
- The checkbox was added for checking or unchecking all the data
  with the same Sync. Group label as the currently selected window.
- The Align All Automatic was added in the Window menu.
  The function aligns all 2D windows from top-left to bottom-right automatically.

7 April 2020
- A bug fix. Extra items for test programs shown in the menu were hidden.

3 April 2020
- Keyboard shortcuts for the mass shift function were added.
1) Shift + Left or Right key: Up or down for the mass shift step
2) Shift + number key (except ten keys): Set the mass shift step to the number
3) Ctrl + Enter: Record the mass shift step number to the comment
4) Ctrl + Del: Clear the comment
5) Ctrl + Shift + / : Record "?" to the comment
6) Enter: Reset the mass shift step to zero and go to the next row

27 March 2020
- Fragment Calculator: Acquisition of the mol file data from HMDB and KEGG
 has been failed due to the change of their URLs to those of HTTPS.
 The issue was fixed.

6 February 2020
- MFSearcher: The link to the KNApSAcK database was changed to the newer one.

- The mass shift function: Preset and fold settings were added.
- Multiple chromatogram files are selectable to open.
- A 2D-mass chromatogram window is open at a bottom-right position of the active window
- Recently opened file and directory are available.
- Alignment function of the 2D-mass chromatogram window:
  The windows are displayed in different positions when they are overlapped.
- Lines starting with "#" or "//" and blank lines are ignored in the Project file.
- Mass Ruler Function:
  "Right shift" and "ppm (always-right)" settings were added.

9 November 2018
- Save/Load project function for the reconstruction of analyzing the environment
  was added.
- Copy/Export function for MSn spectra was improved.
  MS-FINDER (.mat) file can be exported too.
2 December 2017
- The default value for 2D chromatogram color was changed.
  The default color strength is based on 1/10 of the most intense ion.
- The default setting for draw wait was reviewed.
- The default value for load cutoff for MS2Viewer was changed.

29 November 2017
- Toolbar is now available.
- A function to align the 2D windows is added.

2 November 2017
- mzML file is now acceptable.
- Notice of the new version release is added.
- System was modified for the new digit number of HMDB IDs.
- A bug in the proxy setting in the MFSearcher function was fixed.

16 May 2017
- The FlavonoidSearchGUI (FsTool) was integrated.
- System was modified for the change of mol file URLs in HMDB.

16 Jan, 2017
- Now MassChroViewer can run on MacOSX and Linux.

9 January 2017
- The first version for publication with the manual.

25 December 2016
- GUI interfaces were revised.
- Add/Delete function of the peak is available.

23 December 2016
- The direction of mouse wheel operation for the 2D window was reviewed.
- TogoMD-formatted peak-table file is acceptable as a Peak File.
- A simple RT. and m/z data is acceptable as a Peak File.

6 December 2016
- JRAP mzXML parser was replaced with a house-made one for properly
  opening the mzXML files converted with new versions of ProteoWizard
  software. The loading time is remarkably improved too.

3 August 2016
- Search function in the peak table is available.

21 November 2015
- UC2 database is now available in the MFSearcher function.
  To show the concise results where the same constitutional isomers between the
  compound databases were compiled in one record.

17 November 2015
- Now, users can modify the mass ruler settings.
- Data loading and draw wait settings were added for low-spec PCs.
- A function to reset the color strength of the 2D window was added.

4 April 2015
- Keyboard operation for checking peak list was added.