Table 1. Searching with 10 previously identified spectra.

The table lists, for each of the 10 spectra, the scan number, charge state (“+”), number of candidate products (all peptides pairs with every possible link), number of candidate peptide pairs, the two peptides, the inferred location of the cross-linker according to the previous method (“Loc (old)”) and the proposed method (“Loc (new)”), and the q-value assigned to the match. Spectra for which the two methods disagree on the location of the linker are marked with an asterisk in the “Diff” column.

Scan	+	#Prod	#Pairs	Peptide 1	Peptide 2	Loc (old)	Loc (new)	q-val	Diff
1267	4	7	2	kviknvaevk	lymaed	(1, 6)	(4, 6)	0.005	*
1370	4	6	2	fleehpggeevlr	viknvaevk	(4, 3)	(4, 3)	0.005
1605	5	14	2	eqaggdatenfedvghstdar	ysdyfkpfstgkr	(1, 6)	(1, 6)	0.000
1615	5	14	2	eqaggdatenfedvghstdar	ysdyfkpfstgkr	(9, 12)	(9, 6)	0.030	*
1758	5	18	5	eqaggdatenfedvghstdar	ysdyfkpfstgk	(6, 6)	(6, 6)	0.000
1653	4	12	6	fleehpggeevlr	yklcvipr	(3, 2)	(3, 2)	0.000
1654	5	12	6	fleehpggeevlr	yklcvipr	(3, 2)	(4, 2)	0.838	*
1657	5	12	6	fleehpggeevlr	yklcvipr	(3, 2)	(3, 2)	0.000
1658	4	12	6	fleehpggeevlr	yklcvipr	(3, 2)	(3, 2)	0.000
1662	5	12	6	fleehpggeevlr	yklcvipr	(3, 2)	(3, 2)	0.005