How do I use a signing certificate in outgoing messages?

You apply a signing certificate to an outgoing message by adding an encoding component (S/MIME) in the send pipeline. After the component has been added, you configure the component to sign all outgoing messages by clicking True for the Add signing certification to message property. The signing certificate that is used to sign the outgoing message is retrieved from the personal certificate store for the host service account where the pipeline is running.

BizTalk Server supports only one personal certificate for each BizTalk group. A BizTalk group can represent an enterprise, a department, a hub, or another business unit. The personal certificate that is used by the BizTalk group is specified by setting the thumbprint of the personal certificate in the BizTalk group properties.

To enter a thumbprint for the personal certificate for the host service account that is running the pipeline

1. Start BizTalk Server Administration. 2. Right-click the BizTalk group that you want, click Properties, and then click Certificates. 3. In the Thumbprint box, type the thumbprint of the private key certificate that is used to digitally sign outgoing messages from this group. The certificate thumbprint has the following format (where H is a hexadecimal digit): HHHH HHHH HHHH HHHH HHHHH HHHHH HHHHH HHHHH HHHHH HHHHH 4. Click OK.

Source: Microsoft