We are running SQL Server 2008 with currently around 50 databases of varying size and workload. Occasionally SQL Server spikes the CPU completely for about a minute, after which it drops to normal baseline load.
My problem is that I can't determine which database or connection is causing it (I'm fairly sure it is one specific query that is missing an index - or something like that). I have found T-SQL queries that gives you a frozen image of current processes. There are also the "recent expensive queries" view and of course the profiler, but it is hard to map to a "this is the database that is causing it" answer. What makes it even harder is that the problem disappears before I have even fired up the profiler or activity monitor, and it only happens about once or twice a day.
Ideally I would like to use a performance counter so I could simply run it for a day or two and then take a look at what caused the spikes. I can however not find any relevant counter.
Any suggestions?