You can't. Apple's fairplay technology is proprietary and you can't convert a simple MP3 into Apple's protected m4p format. But you don't need to. Genius works with mp3, aac, protected aac formats, etc, all those supported by iTunes. I've been using it on my Mac and my iPhone for a while, with a huge range of files, and very few of them are from the iTunes Store. So I don't know why you're making the assumption that they need to be protected...
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and victorious in war shall be made glorious in peace.