Poster Presentation HUPO 2019 - 18th Human Proteome Organization World Congress

Mass++ ver.4: an open-source, simple and extensible MS data viewer (#880)

Satoshi Tanaka 1 , Masaki Murase 2 , Masaki Kato 2 , Tsuyoshi Tabata 2 , Maiko Kusano 3 , Shin Kawano 4 , Susumu Goto 5 , Yasushi Ishihama 2 , Akiyasu C Yoshizawa 2
  1. Trans-IT, Kaminokawa-machi, TOTIGI [TOCHIGI], Japan
  2. Grad. School of Pharma. Sci., Kyoto Univ., Kyoto, Japan
  3. Res. Inst. of Environ. Med., Nagoya Univ, Nagoya, Japan
  4. Toyama Intl. Univ., Toyama, Japan
  5. DBCLS, DS, ROIS, Kashiwa, Japan


We had developed a software platform “Mass++,” which integrates multiple functions including viewers and file-open functions for multiple kinds of mass spectrometry raw data on Windows environment (J Proteome Res., 13 (8): 3846-3853 (2014)). Now we are rewriting the entire software without OS-depending libraries for the multiple-OS-platforms as an open-source package; we have completed to implement the data viewer, and continue to develop function for proteome analysis.


Mass++ ver.4 is written in Java instead of C++, which was used for past versions, for effective development of cross-platform software for the maintainability. The plug-in structure, the characteristics of past versions of Mass++, remain in this version.


The current build has the following features; the development is still continuing.

  • Plug-in structure. Easy to extend and/or release function when needed as same as the past versions.
  • Cross-platforms. The current build can run not only on Windows but also on Mac OS/X and Linux, in contrast with the previous versions that could run only on Windows.
  • Currently mzML files, the standard and portable file formats, are readable.
  • Simple-designed viewer. The viewer can display fundamental data for mass spectrometry: mass spectra, chromatograms, and heatmaps.
  • Utilizing external functions. Mass++ can read result files from the external program, Comet, for database search and display the list of identified peptides and the annotation of the identified peaks on the heatmap.


Our present purposes of developing Mass++ ver.4 is to cooperate easily with external software and visualize intermediate results during the analysis process; these are necessary for the effective analysis and rarely implemented in freeware. Mass++ ver.4 is released as a BSD 3-claused open-source software at