ProTools is for audio. You can import MIDI into it, but it's not a full fledged MIDI sequencer. ProTools is the industry standard for digital recording.
Sonar, Cubase, Logic + Performer are best for MIDI sequencing, i.e. writing/composing songs using virtual instruments and MIDI capable hardware. These days they also do digital recording, and they do it quite well.
When it comes to professional recording, it's really more about hardware than it is software. Digidesign, the makers of ProTools, manufacture the industry standard break out boxes, with what is considered the highest quality digital>audio convertors (DACs for short), as well as soundcards that independently process effects and what not.