namespaces

option1.js

(function() {

  angular.module('vcModules')
    .factory('QualityService', QualityService);
  
  QualityService.$inject = ['$rootScope','AppLocalStorage'];
  
  function QualityService($rootScope, AppLocalStorage) {
    var vm = this;
    var foo, bar;
    
    // Things we need to expose to other things :-)
    return {
      professional: professional,
      facility: facility
    };
    
    
    // professional namespace
    function professional() {
      return {
        assignConfig: function() {
          foo = 'professional foo';
          console.log(foo);
        },
        assignQuality: function() {
          bar = 'professional bar';
          console.log(bar);
        }
      };
    }
    
    // facility namespace
    function facility() {
      return {
      assignConfig: function() {
        foo = 'facility foo';
        console.log(foo);
      },
      assignQuality: function() {
        bar = 'facility bar';
        console.log(bar);
      }
    };
  
  }

}
})();

option2.js

(function() {

  angular.module('vcModules')
    .factory('QualityService', QualityService);
  
  QualityService.$inject = ['$rootScope','AppLocalStorage'];
  
  function QualityService($rootScope, AppLocalStorage) {
    var vm = this;
    var foo, bar;
    
    // Things we need to expose to other things :-)
    return {
      professionalAssignConfig: professionalAssignConfig,
      professionalAssignQuality: professionalAssignQuality,
      facilityAssignConfig: facilityAssignConfig,
      facilityAssignQuality: facilityAssignQuality
    };

    function professionalAssignConfig() {
      foo = 'professional foo';
      console.log(foo);
    }
    
    function professionalAssignQuality() {
      bar = 'professional bar';
      console.log(bar);
    }
    
    function facilityAssignConfig() {
      foo = 'facility foo';
      console.log(foo);
    }
    
    function facilityAssignQuality() {
      bar = 'facility bar';
      console.log(bar);
    }
  
  }

})();

I like option2.js better. You can quickly at a glance see what methods are available in the service. Option1.js requires the developer to scroll down to the method to see what's available.