"Generally speaking, atoms can be present in any order. Do not conclude that a particular atom is not present until you have parsed all the atoms in the file.
An exception is the file type atom, which typically identifies the file as a QuickTime movie. If present, this atom precedes any movie atom, movie data, preview, or free space atoms. If you encounter one of these other atom types prior to finding a file type atom, you may assume the file type atom is not present. (This atom is introduced in the QuickTime File Format Specification for 2004, and is not present in QuickTime movie files created prior to 2004)."
So, if there is a ftyp atom, it should be first, and if the first atom isn't a ftyp then there isn't one. The AtomParsely link is handy, that should help with producing a metadata extracting parser