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The end-to-end performance of applications in broadband wireless networks is a key concern from the user perspective. Mobile WiMAX is designed to support a wide range of different applications including media streaming, voice-over- IP (VoIP), video conferencing, and web browsing. All of these applications require different levels of quality of service (QoS) and this imposes a variety of different performance requirements on the WiMAX physical (PHY) and medium access control (MAC) layers. For example, TCP-based applications such as FTP or Web-browsing use automatic-repeat-request (ARQ) to tolerate a relatively high PHY packet error rate (PER), whilst a UDP-based application such as video streaming requires very low PER due to the lack of ARQ. This means that the same WiMAX system configuration needs to be able to provide different performance levels for different types of applications in order to operate efficiently. This paper analyses and compares the performance of a multi-input multi-output (MIMO) mobile WiMAX system in terms of achievable throughput and operating range for different PHY PER requirements. The paper shows that TCP applications can achieve higher throughputs and operating ranges due to higher PER tolerance. It also shows that this important QoS parameter affects the AMC switching points. Cross-layer interaction is required between the PHY and the scheduler in the MAC layer in order to efficiently fulfil the various QoS requirements at the application layer.