I lysed my cells in 1x Laemmli buffer for 2 hours by mistake (the usual time period is 15mins). Would this mistake degrade my samples? I'm looking for phosphoproteins.
Francisco is correct, the SDS and reducing environment should have inhibited any phosphatases present. The only caveat I'd make is the incubation temperature. Was the incubation on ice, RT, or were you heating the sample? If you were heating (as in at +90ºC), you may well have degraded your proteins. Otherwise, all should be well.