There is some consensus that Embedded and HPC domains have to create synergies to face the challenges to create, maintain and optimize software for the future many-core platforms. In this work we show how some HPC performance analysis methods can be successfully adapted to the embedded domain. We propose to use Virtual Prototypes based on Instruction Set Simulators to produce trace files by transparent instrumentation that can be used for post-mortem performance analysis. Transparent instrumentation on ISS kills two birds in one shot: it adds no overhead for trace generation and it solves the problem of trace storage. A virtual prototype is build to generate OTF traces that are later analyzed with Vampir. We show how the performance analysis of the virtual prototype is valuable to optimize a parallel embedded test application, allowing an acceptable speedup factor on 4 processors to be obtained.