Silently modifying an IBM MQ server installation using msiexec

To silently modify an installation using msiexec, set the ADDLOCAL parameter to include the features you want to add, and set the REMOVE parameter to the features you want to remove.

For example if you use ADDLOCAL="JavaMsg" and REMOVE="" it modifies the installation to include the Java Messaging and Web Services feature.

msiexec /i {PRODUCT CODE} /q ADDLOCAL="JavaMsg" REMOVE="" INSTALLATIONNAME="Installation1"

The instructions for msiexec begin here: Advanced installation using msiexec