Table 2.

List of proteins identified in urine from training set using peptide mass fingerprinting

# Spota	P-value	MCD	FSGS	Foldb	Trendc	Protein name	Gene name	UniProt accession no.d	Seq. Cov. (%)	Matched peptides	MASCOT Score
1,064	0.004	0.39	1.67	4.3	Down	Branched-chain-amino-acid aminotransferase, mithocondrial	BCAT2	O15382	19.9	5	42.4
1,070	0.004	0.18	2.04	11.5	Down	Nuclear inhibitor of protein phosphatase I	PPP1R8	Q12972	28.2	7	48.4
1,334	<0.001	1.79	0.44	4.1	Up	Alpha-1-antitrypsin	SERPINA1	P01009	21.3	6	44.6
						Platelet-activating factor receptor	PTAFR	P25105	17.3	5	46.5
						Cyclin-Y	CCNY	Q8ND76	32.6	7	49.8
1,352	<0.001	1.79	0.43	4.2	Up	Alpha-1-antitrypsin	SERPINA1	P01009	49.3	13	51.7
1,354	<0.001	1.77	0.40	4.5	Up	Alpha-1-antitrypsin	SERPINA1	P01009	49.3	18	86.3
						Transmembrane channel-like protein 1	TMC1	Q8TDI8	23.9	15	33.4
1,356	<0.001	1.85	0.38	4.8	Up	Transcription elongation factor 1 homolog	ELOF1	P60002	51.8	7	36.2
1,363	<0.001	1.51	0.59	2.6	Up	Transferrin	TF	P02787	24.5	12	64.9
1,392	0.01	0.31	1.57	5.1	Down	Serum albumin	ALB	P02768	28.1	16	58.6
						Leucine-rich repeat-containing protein C10orf11	c10orf11	Q9H2I8	36.9	6	41.6
1,400	0.005	2.18	0.38	5.7	Up	Serum albumin	ALB	P02768	39.4	21	85.1
1,408	0.006	2.17	0.49	4.4	Up	Serum albumin	ALB	P02768	53.2	31	92.1
1,458	0.002	0.28	1.69	6.1	Down	PEST proteolytic signal-containing nuclear protein	PCNP	Q8WW12	51.7	5	38.6
						Branched-chain -amino-acid aminotransferase, mithocondrial	BCAT2	O15382	19.9	5	42.4
1,460	<0.001	0.25	1.72	7	Down	Leucine-rich repeat-containing protein C10orf11	c10orf11	Q9H2I8	36	9	32.7
						Calretinin	CALB2	P22676	32.1	7	27.9
1,468	<0.001	2.22	0.71	3.1	Up	Serum albumin	ALB	P02768	24.8	21	80.2
						39S Ribosomal protein L17, mithocondrial	MRPL17	Q9NRX2	62.9	9	40
						Humanin-like protein 6	HN6	P0CJ73	100	7	64.1
1,469	<0.001	2.98	0.68	4.4	Up	Serum albumin	ALB	P02768	28.2	25	56.6
						Histatin-3	HTN3	P15516	68.6	4	36.7
7,740	<0.001	1.27	0.49	2.6	Up	Zinc-alpha-2-glycoprotein	AZGP1	P25311			155
7,810	<0.001	1.27	0.49	2.6	Up	Zinc-alpha-2-glycoprotein	AZGP1	P25311	28.9	10	61.9

^aSpot number generated by SameSpots image analysis software, referencing the spots shown on Additional file 2

^bRatio of protein expression between MCD and FSGS

^cUp: up-regulated in MCD compared to FSGS; Down: down-regulated in MCD compared to FSGS

^dAccession number from NCBInr database