PDF Annotation: Can it be done alongside the cloud?

I'm getting an iPad mini in the next few days, and as a student, will be using it to store textbooks. I also want to annotate them, highlight things, the usual stuff. But it'd also be great if I could then sync that to my laptop (also a Mac, but would preferably not use a platform-specific tool).

The problem is that each PDF is >50MB. Are there any PDF apps that sync the metadata, like annotations, separately to the whole PDF, instead of just flattening the whole thing and uploading 50MB multiple times a day?