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bioRxiv · 10.1101/617654

Structure-based validation can drastically under-estimate error rate in proteome-wide cross-linking mass spectrometry studies

Yugandhar, K.·Wang, T.-Y.·Yu, H.
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Abstract

Recent, rapid advances in cross-linking mass spectrometry (XL-MS) has enabled detection of novel protein-protein interactions and their structural dynamics at the proteome scale. Given the importance and scale of the novel interactions identified in these proteome-wide XL-MS studies, thorough quality assessment is critical. Almost all current XL-MS studies validate cross-links against known 3D structures of representative protein complexes. However, current structure validation approach only includes cross-links where both peptides mapped to the 3D structures. Here we provide theoretical and experimental evidence demonstrating this approach can drastically underestimate error rates for proteome-wide XL-MS datasets. Addressing current shortcomings, we propose and demonstrate a comprehensive set of four metrics, including orthogonal experimental validation to thoroughly assess quality of proteome-wide XL-MS datasets.

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Yugandhar, K., Wang, T.-Y., Yu, H.. 2019-04-24. Structure-based validation can drastically under-estimate error rate in proteome-wide cross-linking mass spectrometry studies. https://doi.org/10.1101/617654

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