You need donor serum or PBMCs (from an infected host) to check for antibody production by ELISA or T cell responses (ELISPOT or flow cytometry for cytokine production) for in vitro analysis of immunogenicity. Or else, you need to challenge a preferred host with the proteins or the bacteria itself and then check for antibody or T cell responses in vitro.

You can also do immunogenicity prediction of the protein sequence by online tools such as Easypred and Signisite.

And you can also try following links for other online tools for prediction of MHC binding of the peptides from your protein.

For class I http://www.cbs.dtu.dk/services/NetMHCpan/

For class II http://www.cbs.dtu.dk/services/NetMHCIIpan/

However, it purely depends on the host for which you would like to study the immunogenicity.

Goodluck

Thanks Ramachandramouli Budida.