I used qualitative methodology in my Masters, and mixed methodology in my PhD (with the qualitative elements being completely different to the ones used in my Masters). It involved a fair bit of learning, but was worth it to tailor the methodology to the topic. It is possible to approach a supervisor who has the topic in common with you but not the methodology, although supervisors may feel more comfortable taking on a project that's within their existing field of experience. In my case, I sought external support (from specialised research groups) with my methodology, as I wanted to use an approach my supervisors hadn't used.