These are different tools that are each give different types of information. What questions are you trying to answer that could be addressed with both PCR and mass-spec?
You can use MALDI-TOF as a microbial identification system after a bacterial culture.
Whereas PCR is culture independent method but you have to use specific target primers. In the case of use of 16S or 18S primers, the amplicon has to be sequenced to identify the species. As Katie A Burnette wrote, two different method giving different information.