The Kazusa Metabolomics Portal



The ShiftedIonsFinder is an analytical tool (GUI program) for finding peaks having specified mass differences by comparing the mass spectra in two data sets obtained using chromatography-accurate mass spectrometry. This tool enables the user to select candidate labeled peaks by comparing a sample that is labeled with a stable isotope with an unlabeled sample. It is also easy to select peaks that may have been modified by hydration, glycosylation, or acylation. Since the search results can be output in Excel or text file format, the user can perform further analysis or edit the list as needed.

Operating Environment:

The application software was developed using the Java programming language. The Java Runtime Environment (JRE) is required to run a Java program. The JRE must be installed in PC environments where it has not already been installed or where an earlier version than JRE version 1.6.0_10 set forth in this specification is installed. The recommended environment is as follows:

  • OS: Windows XP or above, MacOS X (ver. 10.9 was used for an operation check)
  • CPU: Intel Core 2 Duo equivalent or above
  • Memory: 512 MB or above (depending on processed files)
  • Java: JRE Version 1.6.0_10 or above


ShiftedIonsFinder 1.1.6 (10.1 MB)

* Click once and wait for a while. Due to the security checking system of the server, it may take ~90 seconds to start downloading.


Decompress the zip file, and move the generated folder "ShiftedIonsFinder_*.*.*.*" to any folder on your local drive. Double click the file "launch.bat" in the folder to run the software.


ShiftedIonsFinder 1.1.6 User's Manual (English) (1.40 MB)

*The same manual is included in the tool. Click [Help] -> [Open Manual] menu on the main window to see the manual.


ShiftedIonsFinder: A standalone Java tool for finding peaks with specified mass differences by comparing mass spectra of isotope-labeled and unlabeled data sets.
Kera K, Ogata Y, Ara T, Nagashima Y, Shimada N, Sakurai N, Shibata D, Suzuki H
Plant Biotechnology (2014) 31: 269-274


Use the following permanent URL to link to ShiftedIonsFinder. Don't use the URL of this web page. It might be changed.


Contact Information:

Kota Kera, E-mail: kera AT kazusa.or.jp

Terms of Use:

  1. This application software will be used for research purposes only. It is available for commercial use at a cost to be negotiated with Kazusa DNA Research Institute (referred to as "the Institute" hereinafter) on a case-by-case basis. Partial rights may be requested.
  2. This application software will be used only by the laboratory of the requester, and will not be transferred to a third party.
  3. When publishing research results obtained by using this application software, it will be clearly noted that the application software provided by this Institute was used.
  4. This application software is provided free of charge, and the Institute makes no guarantees regarding its performance. Furthermore, the Institute is not in any way responsible for damages incurred due to either the use of or the inability to use this application software.