Aug. 8, 2014: The first paper introducing “Mass++” was published

“Mass++” is freeware that can analyze data acquired from various mass spectrometry devices.

The first paper describing “Mass++” features was published in “Journal of Proteome Research”.

Features described in the paper are listed below.

  • – Mass++ supports common formats such as mzXML, mzML and netCDF as well as various instrument data formats such as LCMSsolution, GCMSsolution (Shimadzu), Launchpad (Kratos), Xcalibur (Thermo Scientific), Analyst, Analyst QS (AB Sciex), MassLynx (Waters), and MassHunter (Agilent).
  • – Mass++ has rich viewers such as a waveform viewer, a heat map viewer, and a 3D viewer.
  • – Mass++ supports both LC/MS data and MALDI data, which is useful for glycan analysis.
  • – Mass++ supports protein search engines (i.e., Mascot and X! Tandem) and MassBank, which is a metabolite database and search engine, so proteomics and metabolomics analysis can be performed on the same platform.
  • – Mass++ has a plug-in structure that facilitates customizing such as adding new functions and deleting unnecessary functions.
    Developers can add new algorithms or automation systems by new plug-in development without editing the Mass++ source code.
  • – Mass++ supports MSB format, which is an original and lossless format that improves performance of generating chromatograms such as XIC and BPC. A data file in this format stores spectrum and chromatogram data divided into data blocks, thus any given data block can be accessed directly.

Satoshi Tanaka1, Yuichiro Fujita1, Howell E. Parry1, Akiyasu C. Yoshizawa1, Kentaro Morimoto1, Masaki Murase1, Yoshihiro Yamada1, Jingwen Yao1, Shinichi Utsunomiya1, Shigeki Kajihara1, Mitsuru Fukuda2,3, Masayuki Ikawa2,3, Tsuyoshi Tabata2, Kentaro Takahashi2, Ken Aoshima2, Yoshito Nihei4, Takaaki Nishioka4, Yoshiya Oda2, Koichi Tanaka1
“Mass++: A visualization and analysis tool for mass spectrometry”
Journal of Proteome Research, Vol. 13, Issue 8, pp3846-3853

1 Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation
2 Eisai Product Creation Systems, Eisai Co., Ltd.
3 iBioTech Corporation
4 Graduate School of Information Science, Nara Institute of Science and Technology


Link to introduction site of the paper in “Journal of Proteome Research” :

Mass++ site :


Related Topics :
Jun. 10, 2014: Database “ProteinCarta” for protein identification with short terminal sequences is released on the web.
Jun. 10, 2014: Web application “PTM Librarian” for displaying literature information of protein modifications is released.
May. 15, 2014: Mass++ beginners’ guide has been released.
Mar. 27, 2014: Mass++ analysis software upgrade released.