Has the protein composition (with identification) in honey and other honeybee byproducts been studied?
First of all: Honey is not a byproduct of bees - it's their main and most important product which stores energy for the bee hive for the time when no flowers are available.

Honey itself consists (according to the USDA database) to about 99.5% of water and sugars (82.5% sugars, 17% water). The sugars are mostly fructose and glucose, but also some other mono- di and tri-saccherides in traces. See reference 1 for details. It also contains trace amounts of vitamins and minerals, see table from the Wikipedia on Honey:



The protein content varies between honey sample but is somewhere in the range between 0.2 and 0.5% (see also reference 1). The proteins come from flowers (pollen incorporated into the honey) as well as from the bees (see reference 2). Paper 1 lists a number of enzymes as most common bee proteins in the honey, but doesn't go into much more details here. These are invertase, diastase, glucose oxidase and catalase. 

You could now go into the sequence databases (Apis mellifera has been complete sequenced) and look up the sequence information of the enzymes. Information can be found here and here.

References:


A review of the analytical methods to determine the geographical and
botanical origin of honey
Source of the honey protein responsible for apple juice
clarification