The R2TP/Prefoldin-like (R2TP/PFDL) complex is a cochaperone complex involved in the assembly of a number of critical protein complexes. Here we use stable isotope labeling with amino acids in cell culture (SILAC) and FLAG tag affinity purification coupled to mass spectrometry to assess whether siRNA-driven knockdown of cofactors or subunits of R2TP/PFDN affects composition of U5 snRNP and TSC complex.