My understanding of MSTP is that you can map several VLANs to an instance of spanning tree, and have many instances of spanning tree running at a time. I did a bit of reading on Cisco's website, so I'll try to give you my interpretation of what I read. I am assuming that what you are trying to do is capture spanning tree frames, and see if VLAN to instance mappings are correct. I'm not sure that you can do this directly. The reason why, is that the instance mappings are not passed through the BPDUs. From Cisco:
The exact VLANs-to-instance mapping is not propagated in the BPDU, because the switches only need to know whether they are in the same region as a neighbor
I may be missing something, but from what I'm reading, you need to configure each switch in your MSTP region the same as far as the VLAN to instance mappings. From Cisco:
For switches to participate in multiple spanning-tree (MST) instances, you must consistently configure the switches with the same MST configuration information. A collection of interconnected switches that have the same MST configuration comprises an MST region
The configuration digest information of the MSTP BPDU is apparently a calculation that is made by the originating switch from it's VLAN to instance mappings table. I believe that if they are the same value, they belong to the same region, however, the documentation I am reading does not explicitly state that.
At the beginning of this post, I stated that I was not sure that you can directly see if the VLAN to instance mappings are correct by analyzing the BPDUs. If I am correct that the configuration digest values within a common region must match, then yes, you could look at the BPDUs and see if the frames are matching up with frames from another switch in the region.