Affinity purification in combination with isotope labeling of proteins has proven to be a powerful method to discriminate specific from non-specific interactors. However, in the standard SILAC (Stable isotope labeling by amino acids in cell culture) approach dynamic components may easily be assigned as non-specific. We compared two affinity purification protocols, which in combination revealed information on the dynamics of protein complexes. We focused on the central component in eukaryotic transcription, the human TATA binding protein (TBP), which is involved in different complexes. All known TBP associated factors (TAFs) were detected as specific interactors. Interestingly, one of them, BTAF1, exchanged significantly in cell extracts during the affinity purification. The other TAFs did not display this behavior. Cell cycle synchronization showed that BTAF1 exchange was regulated during mitosis. The combination of the two affinity purification protocols allows a quantitative approach to identify transient components in any protein complex.