Instrument, but missing bag (4)
I believe the answer is:
sack
'bag' is the definition.
(both can mean a container)
'instrument but missing' is the wordplay.
'instrument' becomes 'sackbut' (early type of trombone).
'missing' is a deletion indicator.
'sackbut' with 'but' removed is 'SACK'.
(Other definitions for sack that I've seen before include "Destruction" , "Large canvas bag" , "Large bag; dismiss" , "Fire the old drink?" , "present holder" .)