Publish profile files are a new feature of SSDT database projects that enable you to package up all environment-specific properties into a single file for use at publish time; I have written about them before at Publish Profile Files in SQL Server Data Tools (SSDT) and if it wasn’t obvious from that blog post, I’m a big fan!
As I have used Publish Profile files more and more I have realised that there may be times when you need to edit those Publish profile files during your build process, you may think of such an operation as a kind of pre-processor step. In my case I have a sqlcmd variable called DeployTag, it holds a value representing the current build number that later gets inserted into a table using a Post-Deployment script (that’s a technique that I wrote about in Implementing SQL Server solutions using Visual Studio 2010 Database Projects – a compendium of project experiences – search for “Putting a build number into the DB”).
Here are the contents of my Publish Profile file (simplified for demo purposes) :

Notice that DeployTag defaults to “UNKNOWN”.
On my current project we are using msbuild scripts to control what gets built and what I want to do is take the build number from our build engine and edit the Publish profile files accordingly. Here is the pertinent portion of the the msbuild script I came up with to do that:
<ItemGroup>
<Namespaces Include="myns">
<Prefix>myns</Prefix>
<Uri>http://schemas.microsoft.com/developer/msbuild/2003</Uri>
</Namespaces>
</ItemGroup>
<Target Name="UpdateBuildNumber">
<ItemGroup>
<SSDTPublishFiles Include="$(DESTINATION)\**\$(CONFIGURATION)\**\*.publish.xml" />
</ItemGroup>
<MSBuild.ExtensionPack.Xml.XmlFile Condition="%(SSDTPublishFiles.Identity) != ''"
TaskAction="UpdateElement"
File="%(SSDTPublishFiles.Identity)"
Namespaces="@(Namespaces)"
XPath="//myns:SqlCmdVariable[@Include='DeployTag']/myns:Value"
InnerText="$(BuildNumber)"/>
</Target>
The important bits here are the definition of the namespace http://schemas.microsoft.com/developer/msbuild/2003:

and the XPath expression //myns:SqlCmdVariable[@Include='DeployTag']/myns:Value:

Some extra info:
Hope this is useful!
@Jamiet