OS X El Capitan: About excluding system files from backups
You can exclude OS X system files and apps from a Time Machine backup. This saves space, but makes it harder to restore your entire system if your startup disk is damaged and must be repaired or replaced.
OS X system files include the System folder and the apps that come with your Mac, such as Safari, Mail, Messages, iTunes, Dashboard, and others.
To exclude items other than OS X system files, open Time Machine preferences and click the Options button. To open Time Machine preferences, choose Apple menu > System Preferences, then click Time Machine.
If you need to restore your OS X system, and you haven’t backed it up with Time Machine, see Reinstall OS X.