I'll forward this thread to the quota team to see if they know better, but from what I see in the API, there is no "quota" object that you can interact with. Only quota rules which then have a list of users.
A word of caution. This call will patch every quota rule that has the user fred listed in it. But if it's one to one, then that will do what you want. The quota team figured this was basically what the PowerShell Toolkit was doing behind the scenes since they didn't know of any API that was user based as the command would suggest.