When you are working with multiple time-based systems, such as Pro Tools and an external deck, you want both systems to be synchronized. Synchronization is where one system outputs clock source (such as timecode or MIDI Beat Clock) and another device synchronizes to or follows that clock source so that they work together. Pro Tools can be synchronized to other devices (or other devices can be synchronized to Pro Tools) using SMPTE/EBU timecode or MIDI Timecode.
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For more information on different SMPTE/EBU formats, and other concepts related to timecode, see the Pro Tools Sync & Surround Concepts Guide.