Inevitably, mobile applications and services on a growing scale assist us in our daily life situations, fulfilling our needs for leisure, entertainment, communication or information. However, user acceptance of a mobile application depends on the application's perceived quality of experience (QoE) and it also includes the criticality of the application to the user's context and situation at hand. Statistics for usage of mobile applications provided via ‘app stores' show that more than 50% of these applications never reach a minimal required user acceptance level, and get removed from the store. However, despite the importance of understanding of the mobile user QoE, a sound methodology for evaluation of this experience, and of factors influencing it, does not exist. Moreover, this QoE relates to the level of quality of service (QoS) provided by the underlying service and network infrastructures, which usually is provided at ‘best-effort' level. Therefore, in our research we aim to provide a set of rigorous and robust methodological steps to be taken to quantify a mobile user QoE in his natural environments and different contexts, and to analyze its relation with the underlying QoS. We aim to evaluate the applicability if the methodology in a large scale mobile user study for a set of widely used mobile applications.