If you don't already have WiX installed, download the latest version from:
http://wix.sourceforge.net/releases/

1) Copy your certificate into the 'Source' folder. It doesn't have to be named 'SecurityCertificate.cer', but you will need to edit the WXS file if the filename is different (see step 2).
   
   N.B. The included certificate is just an example and can be deleted.

2) Open 'Product.wxs' in Notepad and change the values for the following three variables.

   ProductName      - This is the name that will show up in Add/Remove Programs (XP) or Programs & Features (Vista/7 or newer)
   ManufacturerName - The name of your school/college or company
   CertFileName     - The filename of the certificate. If yours is called 'SecurityCertificate.cer' you won't need to modifiy this value.

3) Run _MakeMSI.cmd to create the MSI.