We recently developed a shotgun tool for cross-linking sites analysis, X!Link, for the sensitive and high-throughput analysis of chemically cross-linked proteins or multiprotein complexes (J. Proteome Res. 2007, 6, 3908-3917). Here, we report a further development of the tool using a probability-based scoring system. It calculates explicit E-values, with which sensitive detection of the cross-links is possible with very low false positives, and now can be applied to moderate numbers of protein sequences. Most of the false positives in large scale analysis originate from partial matching where one side of the peptides is correctly matched while the other side is incorrectly matched. Additional E-values were calculated for each peptide and effectively minimized false positives from such partial matching. The usefulness of the new scoring system was demonstrated for a previously published dataset from a cross-linked cytochrome c protein, searching against a large database of equine protein sequences.