Transcription factors (TFs) are proteins that bind to DNA and regulate gene expression. To understand details of gene regulation, characterizing TF binding sites in different cell types, diseases and among individuals is essential. However, sometimes TF binding can only be measured from biological samples that contain multiple cell or tissue types. Sample heterogeneity can have a considerable effect on TF binding site detection. While manual separation techniques can be used to isolate a cell type of interest from heterogeneous samples, such techniques are challenging and can change intra-cellular interactions, including protein-DNA binding. Computational deconvolution methods have emerged as an alternative strategy to study heterogeneous samples and numerous methods have been proposed to analyze gene expression. However, no computational method exists to deconvolve cell type specific TF binding from heterogeneous samples.