What do you want to analyze? If you want to know which peak is which, then you can run the purified proteins as standards on the same column to identify them. Alternatively, you can measure each enzyme activity in each peak to find out which peak is which enzyme.
Not sure what sample matrix that is. It sounds like you may have all manner of other proteins in there. As a rule of thumb, for SEC to be able to separate your protein cleanly, you need to not have other proteins in +/- 30%-ish of its Mw. And that's only if you can make an optimal choice of exclusion range. In practice, it's often worse. Take samples and analyze by SDS-PAGE gel. The gels generally have far superior resolution to SEC.