Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs utilizing parallel reaction monitoring (PRM) methods. Skyline was adapted for the analysis of quantitative XL-MS data and as a means for sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study. A PRM transition calculator for cross-linked peptides has been integrated into XLinkDB (http://xlinkdb.gs.washington.edu/xlinkdb/), an online database for the storage and analysis of XL-MS data, to easily generate transition lists for import into Skyline. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.