Theoretically you can access your services like this:
browser.executeAsyncScript(function(callback) {
var service = angular.injector(['MyModule']).get('myService');
service.query({}, function(data) {
callback(data);
});
}).then(function (output) {
console.log(output);
});
And there is an example:
https://github.com/andresdominguez/protractor-meetup/blob/master/test/e2e/api-helper.js