A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry


Juan D Chavez, Jimmy K Eng, Devin K Schweppe, Michelle Cilia, Keith Rivera, Xuefei Zhong, Xia Wu, Terrence Allen, Moshe Khurgel, Akhilesh Kumar, Athanasios Lampropoulos, Mårten Larsson, Shuvadeep Maity, Yaroslav Morozov, Wimal Pathmasiri, Mathew Perez-Neut, Coriness Pineyro-Ruiz, Elizabeth Polina, Stephanie Post, Mark Rider, Dorota Tokmina-Roszyk, Katherine Tyson, Debora Vieira Parrine Sant'Ana, and James E Bruce. 2016. “A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.” PLoS One, 11, 12, Pp. e0167547.


Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. 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. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. 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.