In practical terms if your passport says Peter Michael Roberts and your ticket says Mike Roberts then the TSA is probably going to look at it and figure that you use Mike as a common name. If they question it and you have other documentation that shows that you use Mike all the time they would probably let you go. If, on the other hand, your passport says Peter Michael Roberts but your ticket says Pete Sampras you could have a problem.
The fact that there is a spot on the Nexus application to list nick names leads one to believe that they are aware that people often go by a short form of their name , however I don't think you would have much success convincing them that "Shooter" is an appropriate nick name for travel documents
