PCB Design - Mini Pcie Express to Thunderbolt 1 2/Mini Display
You can not connect a PCIe directly to a Thunderbolt port, it requires a controller chip at each end.  See the description from Wikipedia below.


  Thunderbolt controllers multiplex one or more individual data lanes from connected PCIe and DisplayPort devices for transmission via two duplex Thunderbolt lanes, then de-multiplex them for use by PCIe and DisplayPort devices on the other end.


The picture below from an Intel Thunderbolt Technology Brief shows the connectivity described above.