As of November 2020, there are four versions of Mass++ available. Here is a brief summary of the differences.  


Ver. 2.7.4 (developed by Shimadzu Corporation and Eisai Co., Ltd.) is the last version (for now) to be developed with public research funding and is closed source. 


Ver. 2.7.5 is the open source version of Ver. 2.7.4. At this stage, these two function were removed:  

  •     Mass spectrometer vendor-specific file format (raw data) read capability   
  •     Features related to software patents obtained while receiving public research funding   

Please refer to the OSDN page for more information on the differences between these two versions. In this table, “Binary Edition” means “Ver. 2.7.4” and “OSS Edition” means “Ver. 2.7.5”. 


Since Microsoft had stopped distributing development libraries, these versions cannot be improved, bug fixes, etc. in the future. 


Ver. 4 is a version under development that is being rewritten based on a new concept. As of November 2020, there are two versions of Ver.4 Alpha and Ver.4 Beta released. In addition to bug fixes, Ver. 4Beta adds features to Alpha. The differences between these features are as follows:  





Viewer of TIC 



Viewer of XIC 



Viewer of MS1 spectrum 



Viewer of MS/MS spectrum 



Viewer of 2D-heatmap 



Viewer of 3D-heatmap 



Viewer of mirror view for spectra / chromatograms 



Overlapping spectra / chromatograms 



External software execution / data exchange (*) 



Data annotation display (**) 

✓ (Requires manual opereation) 


Supported file format 

mzML, MGF,  
pepXML (Manual file-read only) 

mzML, MGF,  
pepXML (Automatic file-read after the search complete) 

Supported peak-picking program 


ProteoWizard ver. 3.0.20123    
[Windows version only] 

Supported search engine for peptide identification 


Comet ver. 2019.01 rev. 5 
[Windows version only] 

Supported OS 

Windows, macOS 

Windows, macOS, Linux Debian/Ubuntu, Linux RPM 

(*) …. Users can set parameters for external programs, automatically retrieve results from the external program, and input the results into other external programs.  
(Example of its application) 

Peaks were picked from mzML-formatted data and the results are processed to generate a MS/MS peaklist file in Mascot Generic Format (MGF) with the MSConvert program in ProteoWizard. The peaklist is automatically read into Mass++. This peaklist was input into Comet search engine to search against the sequence database, and the search results were output in the pepXML-formatted file. 

(**) …. (example of its application) 

Specify the peptide identification result on the “project” tab in the top panel, and mark the corresponding mass peak on the 2D or 3D heatmap display. 

(another example of its application)  

The XIC of the precursor ion (corresponding to the specified peptide) can be displayed.