Tips: What to do when a spectrum is not displayed?

Q. Spectrum may not be displayed when opening an MS data (mzML) larger than 1GB in size. [Ver.4 alpha, beta]

A.

First check to see if it is possible to open MS data smaller than 1GB (e.g. small.pwiz.1.1.mzML distributed by ProteoWizard). If the spectrum can be displayed, the upper limit of the memory size (the heap size) that Mass++ can allocate is probably insufficient to load the desired MS data.

If you have enough memory in your PC, and you can allocate a larger memory to Mass++, you may be able to display a spectrum by increasing the upper limit of the heap size in the following way; after that, restart Mass++, delete the corresponding MS raw data from Mass++, import it again, and then display it.

– For Windows

Change the setting value of the -Xmx option in C:\Program Files\mspp4\mspp4.bat to an appropriate size. For example, if you want to set the size to 8GB, change it as follows:

“C:\Program Files\mspp4\jre8\bin\java.exe” -Xms1024m -Xmx8g -jar “C:\Program Files\mspp4\mspp-4.0.0_beta.jar”

(If administrator privileges are required for rewriting the file, please rewrite as an administrator.)

– For macOS and Linux

Change the setting value of the -Xmx option in the [JVMOptions] section of the Mass++.cfg file to the appropriate size. For example, if you want to set the size to 8GB, change it as follows:

[JVMOptions]

-Xmx8g

The location of the Mass++.cfg file is as follows:

macOS: Applications folder (Mass++.app)/Contents/Java/Mass++.cfg  

(Select Mass++ in the Finder, right-click to open the context menu and select “Show Package Contents” to handle the contents of the application folder in the Finder.)

Linux: /opt/Mass++/app/Mass++.cfg

(You need administrative privileges to rewrite Mass++.cfg.)