We used a reverse chromatin immunoprecipitation (ChIP) method that takes advantage of the RNA-mediated DNA-targeting capability of Cas9 to efficiently and adaptably isolate specific genomic regions and their associated protein factors. By using purified recombinant catalytically-dead Cas9 (dCas9) combined with single-guide RNAs (sgRNAs) to form specific ribonucleoprotein (RNP) complexes, our method does not require specialized cell lines and can be easily modified to target multiple loci in any cell line or tissue. We have applied this dCas9-based system to identify novel factors involved in D. melanogaster histone cluster (HisC) gene expression. Chromatin-associated proteins were purified by dCas9-HisC revChIP (using eight different sgRNAs of H2A and H2B genomic targets) and were analyzed by MudPIT mass spectrometry. A control dCas9 revChIP using non-specific sgRNAs was analyzed in parallel. In brief, TCA-precipitated protein eluates were urea-denatured, reduced, alkylated, and digested with endoproteinase LysC followed by trypsin. The peptide mixtures were loaded onto microcapillary fused silica columns (100um i.d.), placed in-line with an Agilent 11000 quaternary pump, and analyzed by a 10-step MudPIT on linear ion traps. MS/MS datasets were searched using ProLuCID (v. 1.3.3) (Xu et al., 2015) against a D. melanogaster non-redundant protein database (NCBI, 02-20-2013) containing 160 usual contaminants (human keratins, IgGs, and proteolytic enzymes). To estimate false discover rates (FDRs), the amino acid sequence of each non-redundant protein was randomized. Peptide/spectrum matches were sorted and selected using DTASelect (Tabb et al., 2002) with the following criteria set: spectra/peptide matches were retained only if they had a DeltCn of at least 0.8, and minimum XCorr of 1.8 for singly, 2.0 for doubly, and 3.0 for triply charged spectra. Additionally, the peptides had to be minimum 7 amino acids in length and fully tryptic. Peptide hits from multiple runs were compared using CONTRAST (Tabb et al., 2002). The distributed normalized spectral abundance factors (dNSAF) were used to estimate relative protein levels (Zhang et al., 2010).