Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

Iacobucci, C.; Piotrowski, C.; Aebersold, R.; Amaral, B. C.; Andrews, P.; Borchers, C.; Brodie, N. I.; Bruce, J. E.; Chaignepain, S.; Chavez, J. D.; Claverol, S.; Cox, J.; Degliesposti, G.; Dong, M. Q.; Edinger, N.; Emanuelsson, C.; Gay, M.; Goetze, M.; Gozzo, F. C.; Gutierrez, C.; Haupt, C.; Heck, A. J. R.; Herzog, F.; Huang, L.; Hoopmann, M. R.; Kalisman, N.; Klykov, O.; Kukacka, Z.; Liu, F.; MacCoss, M. J.; Mechtler, K.; Mesika, R.; Moritz, R. L.; Nagaraj, N.; Nesati, V.; Ninnis, R.; Novak, P.; O'Reilly, F. J.; Pelzing, M.; Petrotchenko, E.; Piersimoni, L.; Plasencia, M.; Pukala, T.; Rand,

doi:10.1101/424697

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bioRxiv · 10.1101/424697

Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

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Abstract

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has largely increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats that are generally accepted in the field and that have shown to lead to high-quality results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. From the results obtained, common protocols will be established. Our study serves as basis for establishing best practice guidelines in the field for conducting cross-linking experiments, performing data analysis, and reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

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Iacobucci, C., Piotrowski, C., Aebersold, R., Amaral, B. C., Andrews, P., Borchers, C., Brodie, N. I., Bruce, J. E., Chaignepain, S., Chavez, J. D., Claverol, S., Cox, J., Degliesposti, G., Dong, M. Q., Edinger, N., Emanuelsson, C., Gay, M., Goetze, M., Gozzo, F. C., Gutierrez, C., Haupt, C., Heck, A. J. R., Herzog, F., Huang, L., Hoopmann, M. R., Kalisman, N., Klykov, O., Kukacka, Z., Liu, F., MacCoss, M. J., Mechtler, K., Mesika, R., Moritz, R. L., Nagaraj, N., Nesati, V., Ninnis, R., Novak, P., O'Reilly, F. J., Pelzing, M., Petrotchenko, E., Piersimoni, L., Plasencia, M., Pukala, T., Rand,. 2018-09-26. Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines. https://doi.org/10.1101/424697

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