I would like to begin saying that antibiotic resistance and virulence are different aspects of the mycobacterial infection and are regulated differently. If you want to study virulence you should use a different strategy, which does not include antibiotic resistance mechanisms, to avoid misinterpretations.

Anyway, the proteomic response is very complex and multi-dimensional. By comparing two different strains upon the same treatment, you will find different proteins being produced, different proteins being phosphorilated, as well as different post-translaccional modifications occurring. To complete that picture, one should look at the gene expression (mRNA), to see if it matches with the protein production. Due to this complexity, the first thing would be to compare Mtb H37Rv with or without antibiotic treatment, to map the principal proteins. Then, you could repeat the same experiment in Mtb H37Ra with or without antibiotic treatment. Do not forget to collect all mycobacterial proteins: the ones that constitute the bacteria and those that are secreted. It would be also very interesting to look at Mtb strains obtained from clinical isolates, with known resistances to antibiotics.

Another biologically important parameter on which both the strains can be studied, is the response they promote upon infecting macrophages. By simply infecting human or mouse macrophages cell lines with your strains, you will observe different responses of the macrophages at the mRNA and protein levels, with consequences in the survival of the bacteria. This could complement your experiments.

Finally, after selecting a few interesting proteins, you can over-express or repress them, to study their function.

Thanks Paulo, for detailed and very well thought explanation.