Note: nine upset by musical (5)
I believe the answer is:
annie
'musical' is the definition.
(Annie is a Broadway musical)
'note nine upset' is the wordplay.
'note' becomes 'a' (musical note).
'upset' indicates an anagram.
'nine' is an anagram of 'nnie'.
'a'+'nnie'='ANNIE'
'by' is the link.
(Other definitions for annie that I've seen before include "Popular musical about Little Orphan" , "Musical inspired by comic strip" , "Popular stage musical" , "Little Ophan .....; also a musical" , "Cartoon strip orphan" .)