Table 3 Identified urinary peptides that are encoded in the genome of BALB/c but not B6 mice or vice versa.

		Peptide encoded by the allele of strain		Peptide detected in the urine of the indicated mouse strain in MS experiment no. (1–3)
Gene	Peptide sequence	B6J	BALB/cJ	B6	B6/β ₂ m ^−/−	B10	B10.D2	BALB/c
Ces1c	SVFGAPLLKEGASEEETNL	–	+	–	–	n.a.	n.a.	1
Serpina3k	DVAETGTEAAAATGVIGGIRKAVL	+	–	3	n.a.	n.a.	n.a.	n.a.
	DVAETGTEAAAATGVIGGIRKAIL	–	+	–	–	–	–	1, 2
	VAETGTEAAAATGVIGGIRKAI	–	+	–	–	n.a.	n.a.	1
	VAETGTEAAAATGVIGGIRKAIL	–	+	–	–	–	–	1, 2
	VAETGTEAAAATGVIGGIRKAILPAVHFNRP	–	+	–	–	n.a.	n.a.	1
	AAATGVIGGIRKAIL	–	+	–	–	n.a.	n.a.	1
	AAATGVIGGIRKAILPAVHFNRP	–	+	–	–	n.a.	n.a.	1
	AATGVIGGIRKAIL	–	+	–	–	n.a.	n.a.	1
	AATGVIGGIRKAILPAVHFNRP	–	+	–	–	n.a.	n.a.	1
	ATGVIGGIRKAIL	–	+	–	–	n.a.	n.a.	1
	GVIGGIRKAIL	–	+	–	–	n.a.	n.a.	1
	GIRKAILPAVHFNRP	–	+	–	–	n.a.	n.a.	1
	IRKAILPAVHFNRP	–	+	–	–	n.a.	n.a.	1
	IRKAILPAVHFNRPF	–	+	–	–	n.a.	n.a.	1
	IRKAILPAVHFNRPFL	–	+	–	–	n.a.	n.a.	1
	KAILPAVHFNRPF	–	+	–	–	–	–	1, 2
	KAVLPAVcFNRPFL	+	–	–	1	n.a.	n.a.	–
	KAILPAVHFNRPFL	–	+	–	–	n.a.	n.a.	1
	PAVcFNRP	+	–	3	n.a.	n.a.	n.a.	n.a.
	PAVHFNRPF	–	+	–	–	n.a.	n.a.	1
	PAVcFNRPFL	+	–	1	1, 2	2	2	–
	PAVHFNRPFL	–	+	–	–	–	–	1, 2
Serpina3k	IVIYHTSAQSIL	+	–	1, 2	1, 2	2	2	–
	FVIYHTSAQSIL	–	+	–	–	n.a.	n.a.	1

All cysteine residues occurred in a cysteinylated form, that is, they had bound free cysteine via a disulphide bridge. Because the cysteine residues are not encoded in BALB/c mice, this posttranslational modification differs between mouse strains. Refer to Supplementary Table S1 for details about the set-ups of MS experiments (no. 1–3). ‘n.a.’ indicates that the respective mouse strain was not analysed in the experiments that led to the identification of the peptide. Amino-acid residues that differ between B6 and BALB/c mice are underlined.

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