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How to setup a quota for the whole "Mysite" webapplication in sharepoint 2007?

Update:
Is it possible in SharePoint 2010?

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Under my knowledge so you cannot set up the quota for an entire web app.. this is limited to site collection scope only.

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You could do this indirectly by limiting the size of your content databases. Here's an example:

25 Mysites, each with a site collection quota of 2GB. Set your content database up pre-sized to 50GB with auto-grow disabled. Since you have control over the amount of content databases you are dictating how much space that web application can utilize.

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