Table 6. Temporal changes in acute phase proteins and antimicrobial proteins in the bovine whey proteome after intramammary challenge with Streptococcus uberis. Acute phase proteins were identified using the ingenuity pathway analysis database with fold-change (compared to 0 h post challenge, PC) and p-values based on one-way ANOVA (show in italics if not <0.05). Antimicrobial proteins were added for comparison. For proteins with a fold change >10, the time point with strongest up- or down regulation is in bold. Values >10 are rounded to the nearest integer.

UniProt accession	Protein name	Fold change at specified time PC (h)					False discovery rate adjusted p-value at specified time PC (h)
		36	42	57	81	312	36	42	57	81	312
Acute phase proteins
Q3SZR3	Alpha-1-acid glycoprotein	1.6	1.8	1.8	1.8	1.2	1 × 10 –1	6 × 10 –2	5 × 10 –2	5 × 10 –2	5 × 10 –1
P28800	Alpha-2-antiplasmin	4.9	5.9	4.6	3.1	1.4	4 × 10–5	8 × 10–6	7 × 10–5	2 × 10–3	4 × 10 –1
P12763	Alpha-2-HS-glycoprotein	1.4	1.8	1.7	1.2	–1.4	6 × 10 –2	3 × 10–3	6 × 10–3	4 × 10 –1	6 × 10 –2
Q7SIH1	Alpha-2-macroglobulin	68	170	128	102	33	2 × 10–4	2 × 10–5	4 × 10–5	7 × 10–5	2 × 10–3
P15497	Apolipoprotein A-I	6.3	8.0	6.8	4.1	1.5	3 × 10–5	5 × 10–6	2 × 10–5	7 × 10–4	3 × 10 –1
P81644	Apolipoprotein A-II	11	22	14	5.1	–1.4	4 × 10–2	1 × 10–2	3 × 10–2	2 × 10 –1	8 × 10 –1
Q0VCX1	Complement C1s subcomponent	1.0	1.0	2.2	20	31	1 × 10 +0	1 × 10 +0	4 × 10 –1	4 × 10–3	1 × 10–3
Q3SYW2	Complement C2	11	8.7	19	84	81	2 × 10–2	4 × 10–2	6 × 10–3	1 × 10–4	1 × 10–4
Q2UVX4	Complement C3	1.3	1.3	1.3	1.4	2.0	1 × 10 –1	1 × 10 –1	1 × 10 –1	6 × 10 –2	4 × 10–4
F1MY85	Complement C5a anaphylatoxin	32	32	210	129	21	2 × 10–2	2 × 10–2	4 × 10–4	1 × 10–3	3 × 10–2
P81187	Complement factor B	3.2	4.1	7.4	8.2	2.8	1 × 10–4	6 × 10–6	1 × 10–8	4 × 10–9	4 × 10–4
F1N076	CP Protein	3.5	4.2	4.4	3.7	2.9	3 × 10–5	4 × 10–6	3 × 10–6	2 × 10–5	3 × 10–4
P50448	Factor XIIa inhibitor	–2.5	–2.4	–3.0	–3.2	–1.2	6 × 10–3	7 × 10–3	1 × 10–3	6 × 10–4	6 × 10 –1
P02676	Fibrinogen beta chain	1.2	1.9	13	9.9	7.5	8 × 10 –1	2 × 10 –1	2 × 10 –5	1 × 10–6	5 × 10–4
F1MGU7	Fibrinogen gamma-B chain	–1.7	1.1	3.4	2.9	3.1	2 × 10 –1	9 × 10 –1	3 × 10–3	7 × 10–3	5 × 10–3
Q2TBU0	Haptoglobin	997	4794	14 937	28 858	4191	4 × 10–8	5 × 10–10	3 × 10–11	6 × 10–12	7 × 10–10
Q3SZV7	Hemopexin	131	153	170	158	73	5 × 10–6	3 × 10–6	2 × 10–6	3 × 10–6	3 × 10–5
Q3T0D0	Heterogeneous nuclear ribonucleoprotein K	1.0	4.7	2.5	66	1.0	1 × 10 +0	1 × 10 –1	3 × 10 –1	8 × 10 –5	1 × 10 +0
F1MKS5	Histidine-rich glycoprotein	106	775	760	451	30	6 × 10–4	6 × 10–6	7 × 10–6	2 × 10–5	9 × 10–3
F1MNW4	Inter-alpha-trypsin inhibitor heavy chain H2	51	143	78	52	38	3 × 10–3	3 × 10–4	1 × 10–3	3 × 10–3	5 × 10–3
Q3T052	Inter-alpha-trypsin inhibitor heavy chain H4	14	21	34	38	16	5 × 10–3	1 × 10–3	3 × 10–4	2 × 10–4	3 × 10–3
Q0VC51	Interleukin 1 receptor accessory	2.4	2.4	213	267	1.0	3 × 10 –1	2 × 10 –1	5 × 10–8	2 × 10–8	1 × 10 +0
O77482	Interleukin-1 receptor antagonist	30	80	325	176	1.0	2 × 10–4	8 × 10–6	7 × 10–8	5 × 10–7	1 × 10 +0
Q2TBI0	Lipopolysaccharide-binding protein	28	84	395	693	113	2 × 10–4	5 × 10–6	2 × 10–8	4 × 10–9	2 × 10–6
C4T8B4	Pentaxin	13	7.2	45	82	1.0	6 × 10 –2	2 × 10 –1	8 × 10–3	3 × 10–3	1 × 10 +0
P06868	Plasminogen	31	33	76	71	13	2 × 10–2	2 × 10–2	4 × 10–3	4 × 10–3	7 × 10 –2
P00978	Protein AMBP	16	5.1	26	16	1.2	4 × 10–2	2 × 10 –1	2 × 10–2	4 × 10–2	9 × 10 –1
P18902	Retinol-binding protein 4	2.3	2.2	–1.4	2.4	23	4 × 10 –1	4 × 10 –1	7 × 10 –1	4 × 10 –1	2 × 10–3
Q29443	Serotransferrin	4.3	5.4	5.1	4.0	2.2	2 × 10–4	3 × 10–5	5 × 10–5	4 × 10–4	3 × 10–2
A6QPQ2	Serpin A3-8	20	158	246	283	37	3 × 10–2	5 × 10–4	2 × 10–4	2 × 10–4	10 × 10–3
G8JKW7	SERPINA3 Protein	2.7	3.0	2.9	4.0	2.8	2 × 10–3	1 × 10–3	1 × 10–3	8 × 10–5	2 × 10–3
P02769	Serum albumin	1.9	2.2	2.1	1.4	–1.4	6 × 10–3	1 × 10–3	2 × 10–3	2 × 10 –1	1 × 10 –1
F1MMW8	Serum amyloid A protein – M-SAA3.2	20	58	107	358	73	5 × 10–4	1 × 10–7	1 × 10–6	1 × 10–8	4 × 10–6
P35541	Serum amyloid A protein – SAA1	5	49	1178	1926	6.5	1 × 10 –1	2 × 10–3	6 × 10–7	2 × 10–7	1 × 10 –1
Q8SQ28	Serum amyloid A protein – SAA3	93	201	556	1585	220	4 × 10–5	3 × 10–6	2 × 10–7	8 × 10–9	3 × 10–6
Q32L76	Serum amyloid A protein – SAA4	17	66	27	10	2.0	4 × 10–2	3 × 10–3	2 × 10–2	9 × 10 –2	6 × 10 –1
O46375	Transthyretin	2.4	2.2	1.9	1.3	–1.2	3 × 10–3	7 × 10–3	3 × 10–2	3 × 10 –1	5 × 10 –1
Antimicrobial proteins
P22226	Cathelicidin-1	1026	3812	7281	4743	226	3 × 10–8	8 × 10–10	1 × 10–10	4 × 10–10	2 × 10–6
P19660	Cathelicidin-2	78	1159	2104	1683	38	6 × 10–3	4 × 10–5	1 × 10–5	2 × 10–5	2 × 10–2
P33046	Cathelicidin-4	208	2619	4753	2963	175	3 × 10–4	1 × 10–6	3 × 10–7	8 × 10–7	4 × 10–4
P54229	Cathelicidin-5	1444	9209	16 618	11 722	387	2 × 10–8	2 × 10–10	3 × 10–11	8 × 10–11	8 × 10–7
P56425	Cathelicidin-7	1217	8922	11 877	7316	178	2 × 10–6	2 × 10–8	9 × 10–9	3 × 10–8	3 × 10–2
Q8SPP7	Peptidoglycan recognition protein 1	3305	8453	27 479	17 090	291	5 × 10–10	4 × 10–11	2 × 10–12	6 × 10–12	6 × 10–7