Table 1. A comparison of GPM-archived fragment ion intensities and experimentally-determined fragment ion intensities in MRM transitions designed using the GPM database tool.

Table 1 lists GPM-predicted MRM transitions for several peptides from β-Actin (ACTB, swissprot accession number P60709) and Thrombospondin-1 (THBS1, swissprot accession number P07996), and compares fragment ion intensity values archived in the GPM vs experimentally determined average intensity values and SDs, based on 3 repeat experiments. Whether the peptide is considered unique by the GPM MRM prediction tool is noted in the final column

Protein	Peptide Sequence	Q1	Q3	Fragment	Predicted	Average	SD	Unique?
		m/z	m/z	Type	Intensity (GPM)	Intensity (Expt.)
ACTB	AGFAGDDAPR	488.7	630.3	y6	100	100	0	Y
			701.3	y7	46	66.1	0.49	Y
			343.2	y3	61	23.8	0.53	N
			424.7	y8	33	34.6	0.57	N
			276.1	b3	16	60.1	1.72	N
	GYSFTTTAER	566.8	437.2	b4-H2O	20	20.2	0.40	Y
			308.1	b3	37	62.3	0.28	Y
			678.3	y6	100	100	0	N
			912.4	y8	77	53.6	2.10	N
			577.3	y5	50	52.9	0.22	N
	SYELPDGQVITIGNER	895.9	1086.6	y10	13	14.5	0.25	Y
			706.4	y132+	30	83.1	0.72	Y
			1298.7	y12	100	46.1	0.16	N
			475.2	y4	65	100	0	N
			689.4	y6	62	95.1	1.71	N
THBS1	GFLLLASLR	495.3	672.4	y6	41	100	0	Y
			318.2	b3	18	85.0	5.47	Y
			446.3	y4	100	60.3	8.06	N
			559.4	y5	81	68.7	11.0	N
			544.3	b5	77	14.9	0.72	N
	FVFGTTPEDILR	697.7	742.4	y6	100	100	0	Y
			574.8	y102+	79	84.9	0.40	Y
			219.1	a2	87	53.7	1.49	N
			688.9	y12-H2O2+	50	48.4	0.31	N
			565.8	y10-H2O2+	56	29.1	0.89	N
	GGVNDNFQGVLQNVR	808.9	1083.5	b11-H2O	12	0	0.18	Y
			871.4	b9-H2O	12	1.6	0.51	Y
			629.4	y5	100	80.7	0.04	N
			913.5	y8	47	50.8	0.48	N
			785.5	y7	62	100	0	N