Windows Installer Transforms (.mst) can hold alterations from base installation package(.msi) without changing any features or properties of the original .msi file. They are used along with .msi files.

A typical scenario for why to have .mst file: an organization requires different customization of a software for different departments or users (e.g. shortcuts, features etc). With each different .mst file for different department or group of users, the organization get's what they require from the same original product.

Quick Tip: How to run transform(s) file for the .msi package from a command line?

msiexec /i “PackageName.msi” TRANSFORMS=“TransformName1.mst”