what is the pem certificate for?
Is it the server certificate of the ftps host or some sort of client certificate for the user you are using for connection?
You can check this by renaming or copying the PEM to CER extension (is the same file format internally, DER would use a binary coded version of the PEM/CER text format). CER is recognized by Windows as a certificate extension while PEM is not. When opening a CER-extended file in Windows it should display some informations about the certificate like issuer (a DN), validity, serial number, key algorithms, requester (a DN) etc.
When it is the server certificate for the FTPS (via SSL/TLS), you will only need to add the issuer certificate (and their issuing certificates) to your truststore in IS defined as global truststore and you will trust this certificate automatically when it is presented to your server while connection handshaking.
When it is for the user for logging in to the FTPS server this gets more complicated, depends on the fact if you use basic auth with user/password or certificate based auth with certificate and passphrase.