We are a group of scientists interested in the integration of global data sets from various technological approaches most of which involve NGS. During our own studies and upon analyzing published data we have been surprised about the large variability in data quality. This variable data often preclude comparative analyses despite the appealing individual screenshots, which are generally shown in publications. Therefore we set out to develop a numerical QC system that is independent of peak calling and describes the global, as well as the local robustness of enrichment-based NGS profiles. This QC system evaluates the endpoint of the experiment, namely the robustness of the raw profile, which is affected by a multitude of experimental factors, including antibody performance, DNA fragmentation, crosslinking and the performance of the experimenter. To generate a guide for colleagues engaged in these types of experiments we have QC'ed several thousand profiles that can be queried in our NGS QC database. Using the Galaxy link users can easily perform QC analyses of their own profiles and compare the QC indicators with the corresponding ones in the database. We believe that such QC analyses are essential to generate high quality comparable datasets and wish that our colleagues will publish datasets including the QC analysis. For a description of the basic science and bioinformatics work done in our group, which aims at the integration of global analyses to approach a systems biology-driven understanding of the dynamic regulation of phenomena like cell fate acquisition and tumorigenesis, please have a look at our homepage.