The greatest challenge to structural biologists in the post-genomic era is to decipher both stable and transient interactions of protein complexes. In response to this challenge, significant advances in mass spectrometry have been made in the past two years. With the inception of novel approaches targeted at defining interaction partners, stoichiometry and topology, as well as monitoring real-time reactions, mass spectrometry is well placed to contribute to the understanding of dynamic macromolecular complexes.