setTimeout has optional parameters that can be used to pass in arguments into the timed-out function. From the window.setTimeout - MDC Doc Center:

var timeoutID = window.setTimeout(func, delay, [param1, param2, ...]);

Useful for constructors when you want to use a constructor’s method in the setTimeout.

myAnimator.prototype.animate = function() {
  // advance frame
  this.frame++;
  // move element
  this.element.style.left = this.frame + 'px';
  // go to next frame
  if ( this.frame < this.maxFrames ) {
    // inside of setTimeout, this = window
    // pass in this as a parameter for the function
    setTimeout( function( instance ) {
      // instance = this
      instance.animate();
    }, 30, this );
  }
};

setTimeout extra parameters fiddle