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A combination of 3D Micro X-ray fluorescence spectroscopy (3D Micro-XRF) and Micro-XRF was utilized for the investigation of a small collection of highly heterogeneous, partly degraded Dead Sea Scroll parchment samples from known excavation sites. The quantitative combination of the two techniques proves to be suitable for the identification of reliable marker elements which may be used for classification and provenance studies. With 3D Micro-XRF the three-dimensional nature, i.e. the depth resolved elemental composition as well as density variations, of the samples was investigated and bromine could be identified as a suitable marker element. It is shown through a comparison of quantitative and semi-quantitative values for the bromine content derived using both techniques that, for elements which are homogeneously distributed in the sample matrix, quantification with Micro-XRF using a one-layer model is feasible. Thus, the possibility for routine provenance studies using portable Micro-XRF instrumentation on a vast amount of samples, even on site, is obtained through this work.