Chemical cross-linking and mass spectrometry (CX-MS) is a structural technique that has been gaining in popularity with the advent of instruments that provide increased access to high-resolution MS/MS data. The Speicher laboratory is interested in zero-length cross-links, which provide the highest-quality data, but are the most difficult to identify and analyze. A MS sample preparation and data analysis pipeline, including a software package called ZXMiner, has been developed to collect and analyze zero-length CX-MS data to use in molecular modeling experiments. I used this pipeline to examine the peroxiredoxin-6 (PRDX6) enzyme, which prevents oxidative damage in the lung. I found the identified cross-links did not fit the published crystal structure of a catalytic intermediate, which suggests PRDX6 undergoes conformational changes as part of catalysis. A solution structure of PRDX6 was created using this CX-MS data. Next, I performed optimization experiments in order to adapt the ZXMiner data analysis pipeline from the LTQ Orbitrap XL instrument it was created for to a more state-of-the-art Q Exactive Plus instrument in order to expand its ability to probe complex samples. Combined with a new version of ZXMiner, I was able to determine several parameters that improved the quality of cross-link data for erythrocyte membrane white ghost (WG) samples. I combined the cross-links identified in those samples with immunoprecipitation experiments and review of the pertinent literature to determine a topology model for the anion exchanger 1 (AE1) protein, which plays critical roles in CO2 transport and the erythrocyte membrane skeleton. Using this topology model and published crystal structures for the N-terminal domain of AE1, I was able to perform combinatorial modeling experiments which resulted in a model of the full-length protein that resolved several controversies in the field. These results show that zero-length CX-MS is a powerful technique to determine structural information of proteins difficult to interrogate through conventional means.