KOMICS

The Kazusa Metabolomics Portal

 

MassChroViewer

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.

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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

Download:

MassChroViewer_1.5.1.zip (zip compressed: 27.1 MB, Updated on Dec 2, 2017)

Manual:

MassChroViewer_manual_en.pdf (English 2.25 MB)

MassChroViewer_manual_ja.pdf (Japanese 2.45 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.

Publication:

MassChroViewer: A two-dimensional data viewer for quality checking of liquid chromatography mass spectrometry.
Sakurai N, Ara T, Ikeda C, Suda K, Sato M, Akimoto N, Yamada M, Narise T
in preparation

Lisense:

MassChroViewer is available free of charge for academic purpose.