Table II. Effectiveness of Protein Prospector metrics as classifiers of target versus decoy cross-link matches.

Parameter	r coefa	# Targetb	Specificity	Threshold
SVM dvalc	0.581	2349	0.927	0.0
scorediffd	0.544	2258	0.923	8.5
pep2.pExpe	0.441	1405	0.926	−0.2
XL pExpf	0.439	1045	0.926	9.9
pep2.score	0.439	1621	0.925	13.6
Low score	0.430	1785	0.924	15.9
XL score	0.408	1122	0.926	58.3
% TIC matchedg	0.390	1092	0.926	79.6%
pep2.norm_scoreh	0.297	733	0.926	2.4
pep1.pExp	0.280	425	0.924	9.2
pep1.score	0.275	532	0.925	55.3
pep1.norm_score	0.143	342	0.924	4.7
pep1.lengthi	0.104	375	0.926	24
ppm	0.086	NA	NA	NA
z	0.067	NA	NA	NA
mz	0.004	NA	NA	NA
pep2.length	−0.024	NA	NA	NA
pep1.rankj	−0.204	NA	NA	NA
pep2.rank	−0.308	NA	NA	NA

^a Point biserial correlation coefficient between Prospector metric and matches to the target database.

^b Number of spectral matches classified as positive cross-link hits at the given score threshold, chosen to achieve equal specificity (see text).

^c Score of final SVM classifier. Model was trained as described in the text; reported here is the result of the final classification.

^d Difference in score between the top cross-linked match and the top linear match.

^e −log₁₀(Exp_pep2), where Exp_pep2 + expectation value of weaker peptide.

^f −log₁₀(Exp_XL), where XL refers to the complete cross-link.

^g Percentage of total ion current intensity in the peaklist that can be explained by the cross-link.

^h Score normalized by length of peptide.

ⁱ Length of peptide in amino acids.

^j Rank of individual peptide match (e.g. rank 1 indicates top match to spectrum).