The Kazusa Metabolomics Portal



FlavonoidSearch system

FlavonoidSearch is a system for flavonoid annotation using mass spectral data retrieved from tandem mass (MS/MS) or multi-stage mass analysis (MSn) of mass spectrometers. The system consists of a probable mass fragment database constructed manually for known flavonoids (FsDatabase)and a command line tool (FsTool) to search the database.

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Link to this page

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

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/218-flavonoidsearch.html


Akimoto N, Ara T, Nakajima D, Suda K, Ikeda C, Takahashi S, Muneto R, Yamada M, Suzuki H, Shibata D and Sakurai N (2017) FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry, Scientific Reports 7: 1243 (2017)
[Journal website]


Binary raw data, peak list, and MSn data acquired in the paper are available here.

SampleSample Info.
Raw File
Peak table and MSn list
Parsley (green house grown) SE61_S11_M014 MDLC1_47222 download (zip 12.3MB)
Parsley (cultivation shelf grown) SE61_S21_M015 MDLC1_47225 download (zip 594KB)
Apple (fruit) SE62_S01_M5 MDLC1_47226 download (zip 89KB)
Broccoli (edible part) SE62_S02_M5 MDLC1_47227 download (zip 168KB)
Carrot (root) SE62_S03_M5 MDLC1_47228 download (zip 26KB)
Purple carrot (root) SE62_S04_M5 MDLC1_47229 download (zip 213KB)
Chinese cabbage (shoot) SE62_S05_M5 MDLC1_47230 download (zip 32KB)
Eggplant (fruit) SE62_S06_M5 MDLC1_47231 download (zip 230KB)
Grape (flesh) SE62_S07_M5 MDLC1_47232 download (zip 149KB)
Green pepper (fruit) SE62_S08_M5 MDLC1_47233 download (zip 138KB)
Paprika (fruit) SE62_S09_M5 MDLC1_47234 download (zip 115KB)
Mandarin orange (peeled fruit) SE62_S10_M5 MDLC1_47235 download (zip 319KB)
Orange (peeled fruit) SE62_S11_M5 MDLC1_47236 download (zip 378KB)
Onion (edible part) SE62_S12_M5 MDLC1_47237 download (zip 231KB)
Spinach (shoot) SE62_S13_M5 MDLC1_47238 download (zip 256KB)
Squash (fruit) SE62_S14_M5 MDLC1_47239 download (zip 51KB)
Strawberry (fruit) SE62_S15_M5 MDLC1_47240 download (zip 416KB)


This is a tool to search flavonoid aglycones in FsDatabase match to the query spectra. FsTool can be used both as an easy-to-use graphical user interface (GUI) tool and a command line tool for high-throughput calculations on servers.
FlavonoidSearch FsTool GUI

Computer Requirements

Java Runtime Environment (1.6.0 or newer, Oracle Corporation) is required in your PC. See Oracle's website for installation of Java.

We tested the tool using following PCs:
Windows 10, MacOSX, CentOS 7.2 Linux


FlavonoidSearch_FsTool ver.1.2.0 (3.53 MB)


FsTool_tutorial_en.pdf (English, 841 KB)

FsTool_tutorial_ja.pdf (Japanese, 1.09 MB)

User Manual

FsTool_manual_en.pdf (English, 555 KB)

FsTool_manual_ja.pdf (Japanese, 685 KB)


FlavonoidSearch is available free of charge for academic purposes. This software "FlavonoidSearchTool.jar" includes an open source software "flavonoidsearch.jar" which is licensed under the GNU Lesser General Public License, Version 2.1 (LGPL 2.1). The source codes of "flavonoidsearch.jar" is included in the jar file.