Yes you can deploy an msi with Deployment Manager. Deployment Manager by default will not run the msi on the Agent for you. If by deploying you just want to copy the msi to the Agent, then Deployment Manager will do that for you.
If however, you want the msi to be run on the Agent, as part of the deployment, you will need to write some Powershell. Deployment Manager runs powershell scripts before, during and after the deployment. You will need to generate a NuGet package containing the msi and a script called 'Deploy.ps1'. This powershell command will run the installer silently, during deployment, on the Deployment Agent:
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msiexec -i <nameOfTheMsi> /qn
I would recommend reading information here about powershell scripts: http://documentation.red-gate.com/displ ... eployment#
If you would like more help about how to create a NuGet package, please have a look at this page: http://documentation.red-gate.com/displ ... lications#
Hope this helps!