Table IV. Agreement between SRM peptide amounts and IHC scores (A) or FISH ratio categories (B). k factors, p values (for κ factor) and percentage agreement are reported for all six peptides and for all four normalization factors tested. The highest κ factor for prediction of IHC score and FISH category respectively are highlighted in bold characters.

Peptide sequence	Normalization parameter 1 (tumor surface)			Normalization parameter 2 (BCA assay)			Normalization parameter 3 (AUC total ion current)			Normalization parameter 4 (average KRT19 peptides)
	κ factor	p value κ	agreement [%]	κ factor	p value κ	agreement [%]	κ factor	p value κ	agreement [%]	κ factor	p value κ	agreement [%]
A. Agreement of SRM peptide amount with IHC score
ELVSEFSR	0.728	3.3E-06	70.0	0.817	2.1E-07	72.5	0.874	2.9E-08	77.5	0.741	1.7E-06	72.5
FVVIQNEDLGPASPLDSTFYR	0.715	3.5E-06	67.5	0.830	1.5E-07	77.5	0.712	2.6E-06	70.0	0.687	7.5E-06	70.0
GIWIPDGENVK	0.741	1.7E-06	72.5	0.712	2.6E-06	70.0	0.674	8.8E-06	67.5	0.687	7.5E-06	70.0
GLQSLPTHDPSPLQR	0.707	5.3E-06	67.5	0.809	3.0E-07	80.0	0.805	2.7E-07	77.5	0.622	6.0E-05	67.5
SGGGDLTLGLEPSEEEAPR	0.712	2.6E-06	70.0	0.712	2.6E-06	70.0	0.726	2.2E-06	70.0	0.635	2.8E-05	67.5
SLTEILK	0.728	3.3E-06	70.0	0.815	2.4E-07	72.5	0.779	7.6E-07	72.5	0.789	1.9E-07	75.0
B. Agreement of SRM peptide amount with FISH category
ELVSEFSR	0.602	7.0E-05	40.0	0.619	2.8E-05	45.0	0.592	7.6E-05	42.5	0.589	5.8E-05	50.0
FVVIQNEDLGPASPLDSTFYR	0.642	2.6E-05	42.5	0.603	3.9E-05	42.5	0.568	1.5E-04	45.0	0.600	5.5E-05	47.5
GIWIPDGENVK	0.647	2.4E-05	47.5	0.610	4.1E-05	42.5	0.585	9.3E-05	50.0	0.605	4.2E-05	45.0
GLQSLPTHDPSPLQR	0.667	1.2E-05	47.5	0.688	3.3E-06	47.5	0.634	2.9E-05	42.5	0.593	6.8E-05	47.5
SGGGDLTLGLEPSEEEAPR	0.617	4.1E-05	42.5	0.664	9.3E-06	45.0	0.592	7.6E-05	42.5	0.614	3.7E-05	47.5
SLTEILK	0.664	1.2E-05	45.0	0.625	2.3E-05	45.0	0.607	4.4E-05	45.0	0.623	2.5E-05	42.5