LAUSR

Chemical cross-linking and mass spectrometry is of growing use for establishment of distance constraints on protein conformations and interactions. Whereas intra-protein cross-links can arise from proteins in isolation, inter-protein cross-links reflect proximity of two interacting proteins in the sample. Prediction of expected ratios of the number of inter-protein to intra-protein cross-links is hindered by lacking comprehensive knowledge on the interactome network and global occupancy levels for all interacting complex subunits. Here we determine the theoretical number of possible inter- and intra-protein cross-links in available PDB structures of proteins bound in complexes to predict a maximum expected fraction of inter-protein cross-links in large scale in vivo cross-linking studies. We show how the maximum fraction can guide interpretation of reported inter-protein fractions with respect to the extent of sample protein binding, comparing whole cell and lysate cross-linked samples as an example. We also demonstrate how an observation of inter-protein cross-link fractions greater than the maximum value can result from the presence of false positive cross-links which are predominantly inter-protein, their number estimable from the observed surplus fraction of inter-protein cross-links.