Enhancing Inter-link Coverage in Cross-Linking Mass Spectrometry through Context-Sensitive Subgrouping and Decoy Fusion
Bogdanow, B.; Wang, C.; Ruwolt, M.; Ruta, J.; Mühlberg, L.; Zeng, W.-F.; Elofsson, A.; Liu, F.
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In cross-linking mass spectrometry, sensitivity and specificity in assigning mass spectra to cross-links between different proteins (inter-links) remains challenging. Here, we report on limitations of commonly used concatenated target-decoy searches and propose a target-decoy competition strategy on a fused database as a solution. Further, we capitalize on context-divergent error rates by implementing a novel context-sensitive subgrouping strategy. This approach increases inter-link coverage by [~] 30 - 75 % across XL-MS datasets, maintains low error rates, and preserves structural accuracy.
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