Table 2 Verification of SAA variant origins of peptides detected by LC-MS/MS, case 1.

Variant	Position	Sequence	Cortex					Medulla					Papilla
Variant	Position	Sequence	T1	T2	T3	C1	C2	T1	T2	T3	C1	C2	T1	T2	T3	C1	C2
v1, v4	39–45	GNYDAAR	-	-	-			49	43	47			47	43	44
v3	39–46	GNYDAAQR	39	32	36			32	-	-			42	39	39
v1, v3	46–55	RGPGGAWAAK	-	-	-			42	49	43			39	35	-
v1, v3	47–55	GPGGAWAAK	52	63	59			58	64	49			53	65	63
v4	47–55	GPGGVWAAK	-	-	-			-	-	-			-	-	-
v1	42–52	DAARRGPGGAW				-	-				30	30				25	24
v3	42–52	DAAQRGPGGAW				45	48				50	47				51	58
v4	42–52	DAARRGPGGVW				-	-				-	-				-	-
Dominant SAA variant			v3					v1					v1 and v3

Five amyloid deposits—three tryptic samples (T1–T3) and two chymotryptic samples (C1, C2)—were collected from each of the glomeruli, medulla, and papilla, and analyzed by LC-MS/MS. The numbers indicate peptide scores obtained from Mascot analysis. For each peptide, the score represents the highest-scoring spectrum among all matches to the same peptide sequence, reflecting the most confident identification. “–” indicates that the corresponding peptide fragment was not detected. At the bottom of the table, the identified amyloidogenic SAA variant is indicated based on the detected peptide fragments.

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