MSMQT Deprecation
The MSMQT feature has been removed from BizTalk Server 2010. In Orchestration Designer, the MSMQT transport option remains available in the design-time Port Configuration Wizard as shown in the image below when you choose the Specify now option for Port binding. This is a known issue with BizTalk Server 2010.
Port Configuration Wizard showing MSMQT transport
BizTalk Server 2010 Projects
New BizTalk Server projects should not use the MSMQT transport option. Application deployment to BizTalk Server 2010 will fail with the error Protocol type “MSMQT” not found.
BizTalk Server 2006 Projects Migrated To BizTalk Server 2010
BizTalk Server 2006 projects are migrated to BizTalk Server 2010 by using the Visual Studio Conversion Wizard as documented in Migrating a BizTalk Server Project. Projects containing ports configured to use the MSMQT transport with BizTalk Server 2006 must be manually reconfigured before deployment to BizTalk Server 2010. The recommended reconfiguration is to use the MSMQ adapter. For more information about the MSMQ adapter see What Is the MSMQ Adapter?.