You take a -2 penalty on disable device and pick locks checks if you don't have thieves tools, you take a -2 penalty on perform checks if you don't have an instrument, and you take a -2 penalty on heal checks if you don't have a healing kit. If you have a masterwork-quality item, you get a bonus to the skill check.
If you go to the skill page and highlight your skill rank, it will show you all your modifiers. On the applicable skills you'll see a -2 modifier because you lack the appropriate tool/kit/instrument..
