Commission allocations in transaction management of auction-based trading for specialized items such as fixed income instruments. A plurality of workstations that are connected to a server, and a structured commission allocation protocol may be provided. Through the workstations, the server and the commission allocation protocol, the systems and methods may allocate commissions or fees when trading securities at accelerated levels with minimal errors and costs, control commission elements during real-time trading, reward customers and brokers who participate in transactions, and distribute commission and transaction data in real time.