Chemical cross-linking coupled with mass spectrometry, an emerging approach for protein topology and interaction studies, has gained increasing interest in the past few years. A number of recent proof-of-principle studies on model proteins or protein complex systems with improved cross-linking strategies have shown great promise. However, the heterogeneity and low abundance of the cross-linked products as well as data complexity continue to pose enormous challenges for large-scale application of cross-linking approaches. A novel mass spectrometry-cleavable cross-linking strategy embodied in Protein Interaction Reporter (PIR) technology, first reported in 2005, was recently successfully applied for in vivo identification of protein-protein interactions as well as actual regions of the interacting proteins that share close proximity while present within cells. PIR technology holds great promise for achieving the ultimate goal of mapping protein interaction network at systems level using chemical cross-linking. In this review, we will briefly describe the recent progress in the field of chemical cross-linking development with an emphasis on the PIR concepts, its applications and future directions.