Table 1.

List of protein accessions identified in the different milk extracts, along with their description, their coverage (percentage of the database protein sequence covered by matching peptides) across samples, the number of unique peptides (distinct peptide that match to a single protein entry within the search database), the occurrence (%) in the three methods and the two breeds.

No	Description	gi Accession	IPI accession	Σcoverage (%)	Σ# Unique Peptides	Occurrencea in method A (%)	Occurrencea in method B (%)	Occurrencea in method C (%)	Occurrencea in breed H (%)	Occurrencea in breed J (%)
1	11 kDa protein		IPI00843089.3	52.3	22	100	100	100	100	100
2	Actin 1	4501885	IPI00698900.1	16.5	520	72	67	40	47	73
3	Alpha-1-acid glycoprotein	94966811	IPI00691212.1	33.7	10	97	100	27	77	75
4	Alpha-1-antiproteinase	27806941	IPI00695489.1	24.5	10	97	94	85	98	87
5	Alpha-1B-glycoprotein	114053019	IPI00692686.1	13.3	6	9	39	35	41	13
6	Alpha-2-HS-glycoprotein	27806751	IPI00707101.1	19.2	8	86	74	65	90	62
7	Alpha-lactabumin	119393699		30.8	3	95	0	55	50	51
8	Alpha-lactalbumin	505782142		9.9	1	7	0	0	5	0
9	Alpha-lactalbumin	11036986		18.1	2	100	100	100	100	100
10	Alpha-lactalbumin	27805979	IPI00717424.1	31.0	53	55	0	0	18	21
11	Alpha-lactalbumin-like isoform X3	585153938		12.3	3	100	0	0	36	34
12	Alpha-S1-casein	159793227		15.8	1	100	100	100	100	100
13	Alpha-S1-casein	299676		64.7	1	0	1	0	0	1
14	Alpha-S1-casein	162650		14.0	1	22	12	17	22	11
15	Alpha-S1-casein isoform X2	528953236		41.3	47	100	100	100	100	100
16	Alpha-S1-casein isoform X3	528953238		42.2	47	100	100	100	100	100
17	Alpha-S1-casein isoform X6	528953244		30.2	5	100	100	100	100	100
18	Alpha-S1-casein isoform X7	528953246		49.2	47	100	100	100	100	100
19	Alpha-S2-casein	27806963	IPI00698843.1	59.5	29	0	4	10	5	4
20	Alpha-S2-casein	147744646		24.1	1	100	100	100	100	100
21	Angiogenin-1	118151356	IPI00726982.1	31.8	5	76	39	74	69	57
22	Antibody Blv5b8	513137425		9.5	5	51	6	35	41	21
23	Anti-hiv llama vhh antibody a12	380258837		6.3	1	0	0	1	0	1
24	Apolipoprotein A-I preproprotein	75832056	IPI00715548.1	38.1	56	99	0	99	67	63
25	Apolipoprotein A-II	114052298	IPI00688815.2	16.0	5	25	0	0	14	3
26	Apolipoprotein A-IV	82697389	IPI00695965.1	18.7	19	36	0	4	12	16
27	Apolipoprotein E	27806739	IPI00712693.1	7.3	12	75	0	15	30	32
28	ATP-binding cassette sub-family G member 2	112817615	IPI00690408.5	7.9	80	100	0	81	62	59
29	Beta-1,4-galactosyltransferase 1		IPI00760476.26	5.1	2	90	29	0	54	29
30	Beta-1,4-galactosyltransferase 1	116241263	IPI00685910.2	10.0	29	0	0	5	3	0
31	Beta-2-microglobulin	41386683	IPI00686769.1	23.7	22	100	82	97	96	90
32	Beta-casein	555980347	IPI00697085.1	23.7	8	0	0	81	27	23
33	Beta-casein	83406093		23.7	45	0	100	0	32	36
34	Beta-casein variant I	38231527		35.9	2	35	0	0	12	13
35	Beta-lactoglobulin	54037712		37.0	22	1	0	0	0	1
36	Beta-lactoglobulin	562890035		30.0	1	100	100	100	100	100
37	Beta-lactoglobulin	87196497	IPI00699698.1	41.0	18	5	0	19	6	10
38	Beta-lactoglobulin	223165		47.5	19	100	0	100	68	64
39	Beta-lactoglobulin	49259423		47.5	15	100	0	0	36	34
40	Beta-lactoglobulin	378947940		25.8	1	100	100	0	68	70
41	Beta-lactoglobulin A	2194088		47.5	22	100	0	0	36	34
42	Beta-lactoglobulin-like	593730995		9.4	1	22	0	0	2	13
43	Butyrophilin subfamily 1 member A1	3183510	IPI00708535.1	28.1	335	100	100	100	100	100
44	Cathelicidin-1	27807341	IPI00718108.1	10.3	10	6	0	1	5	0
45	Cathelicidin-4	27807337	IPI00686754.1	11.1	1	5	13	1	12	1
46	CD5L protein		IPI00867131.2	14.1	23	25	0	81	22	45
47	CD81 antigen	78042548	IPI00685617.1	6.8	9	89	8	0	37	31
48	Cell division control protein 42 homolog isoform 1	4757952	IPI00704257.2	5.2	76	19	0	33	19	15
49	Chemokine (C-X-C motif) ligand 3	114050915	IPI00721750.2	14.4	9	95	0	0	34	33
50	Clusterin preproprotein	27806907	IPI00694304.1	18.0	53	97	95	99	95	98
51	Complement C3	602697202		7.9	86	100	100	100	100	100
52	Complement C3	124056491	IPI00713505.2	34.0	152	100	0	0	36	34
53	Cysteine-rich secretory protein 3	118601862	IPI00715999.1	23.4	7	99	78	90	91	87
54	dnaJ homolog subfamily B member 9	300795871	IPI01000889.1	17.9	89	0	20	13	8	13
55	dnaJ homolog subfamily C member 3	27807457	IPI00693007.1	3.4	14	0	0	1	1	0
56	Dystroglycan	27806449	IPI00707359.1	1.8	21	0	91	1	32	30
57	Endopin 2B	38683423	IPI01017613.1	16.6	7	92	0	0	35	29
58	Epididymal secretory protein E1	27806881	IPI00711862.1	32.9	8	59	80	8	62	38
59	Fab Pgt123 Hiv-1 Neutralizing Antibody	491668737		5.2	1	56	13	0	34	13
60	Factor XIIa inhibitor	27807349	IPI00710025.1	15.4	7	100	68	71	82	78
61	Fatty acid synthase	426239165		1.2	11	8	0	0	1	5
62	Fatty acid-binding protein	507563106		14.3	40	99	40	100	94	64
63	Fatty acid-binding protein	27805809	IPI00691946.2	47.4	109	80	0	9	34	28
64	Fibrinogen alpha chain	75812954	IPI00691819.1	8.9	7	95	28	63	77	48
65	Fibrinogen beta chain	218931172	IPI00709763.5	11.7	24	27	53	49	49	37
66	Fibroblast growth factor-binding protein 1	27805911	IPI00704023.1	11.5	5	94	40	92	87	63
67	Fibronectin isoform X10	528940100	IPI01028178.1	0.6	484	0	0	3	0	2
68	Folate receptor alpha	330688394	IPI01017673.1	9.1	4	76	74	0	59	44
69	Gelsolin isoform b	296484315	IPI01017675.1	1.8	190	0	11	0	2	5
70	Glutamyltranspeptidase 1 gamma	329664306	IPI00705565.2	6.7	4	10	2	0	2	7
71	Glycosylation-dependent cell adhesion molecule 1	27807339	IPI00716366.1	50.3	39	100	100	100	100	100
72	GTP binding protein Rab1a	15281851	IPI00883580.1	17.0	118	0	1	37	16	8
73	hCG1791766 isoform CRA_a	119626014		13.7	2	0	18	47	22	20
74	Heat shock cognate 71 kDa protein	548494982	IPI00708526.2	5.9	656	14	0	0	4	6
75	Heat shock-related 70 kDa protein 2	148887197	IPI00710052.1	1.7	1	0	1	19	8	5
76	Hedgehog interacting protein-like 2-like	76669880	IPI00700055.2	11.5	10	0	80	96	60	54
77	Hemopexin	77736171	IPI00690198.4	3.5	6	2	0	0	2	0
78	Heparin cofactor 2	157280001	IPI00688367.1	2.6	6	0	5	0	1	2
79	Histatherin	242347807	IPI00944405.1	39.7	2	13	12	88	44	28
80	Hornerin	28557150		4.1	6	0	0	1	0	1
81	Ig anti-HIV-1	612405504		12.6	1	1	0	59	13	25
82	Ig J chain	32401410	IPI00701295.1	29.9	20	99	100	99	98	100
83	Ig lambda light chain	15088675		21.3	10	100	0	100	68	64
84	Ig lambda light chain constant region 2 allotypic variant IGLC2b	343197004		30.2	1	98	100	0	67	69
85	Ig lambda light chain constant region 3 allotypic variant IGLC3c	343197026		52.8	3	100	100	100	100	100
86	Ig lambda-1 variable region	42759882		13.9	2	0	0	19	1	11
87	Ig lambda-like polypeptide 1-like		IPI01002118.1	23.3	8	100	0	100	68	64
88	Ig light chain	310893433		16.7	3	91	62	77	80	74
89	Ig light chain	310893435		61.4	16	100	0	100	68	64
90	Ig light chain variable region	5802436		11.5	1	100	100	100	100	100
91	Ig light chain variable region	2323400		41.8	12	0	4	3	4	0
92	Ig light chain variable region	482673169		9.4	15	16	6	0	10	6
93	Ig light chain, lambda gene cluster	92096965	IPI00867205.1	20.1	1	0	100	0	32	36
94	IgG1 heavy chain constant region	7547266		16.4	9	98	95	99	98	97
95	IgG2a heavy chain constant region	1699167		12.9	2	48	5	45	42	23
96	IGK protein	115545495	IPI00724838.2	10.0	10	0	2	99	34	29
97	IgM heavy chain constant region	2232299		22.7	53	100	100	100	100	100
98	Inhibitor of carbonic anhydrase-like	470655576		5.2	7	0	6	0	3	1
99	Isocitrate dehydrogenase cytoplasmic	75056526	IPI00702781.2	12.1	5	0	0	14	6	2
100	Isocitrate dehydrogenase cytoplasmic	75832090	IPI01028293.1	25.9	148	77	0	0	28	26
101	Kappa-casein	8099324		40.6	33	1	6	13	5	8
102	Kappa-casein	162807		42.4	42	100	100	100	100	100
103	Kappa-casein	1705608		24.0	135	100	100	100	100	100
104	Kappa-casein	284027124		17.3	133	100	54	100	88	81
105	Kappa-casein	315143016		36.8	67	58	26	24	32	41
106	Kappa-casein	428755215		13.6	2	100	100	100	100	100
107	Kappa-casein	428755219		33.3	66	99	100	100	99	100
108	Kappa-casein	284626		58.5	1	100	100	100	100	100
109	Kappa-casein	2493514		20.5	10	100	100	100	100	100
110	Kappa-casein	251198		100.0	1	100	100	100	100	100
111	Kappa-casein	1594249		9.0	2	100	100	0	68	70
112	Kappa-casein A	229416		57.1	33	100	100	100	100	100
113	Kininogen-1	125505	IPI00701166.1	11.6	13	99	0	26	50	36
114	Kininogen-2	490	IPI00718535.1	10.4	4	0	53	0	29	7
115	Kininogen-2 isoform X1	528936694		14.7	17	99	0	0	35	34
116	Lactadherin	2494285	IPI00689035.1	33.3	55	100	62	100	100	75
117	Lactoperoxidase	27806851	IPI00716157.1	26.1	144	36	0	36	23	25
118	Lactoperoxidase	16740670		5.1	12	100	100	100	100	100
119	Lactotransferrin	589925430		4.0	24	100	100	100	100	100
120	Lactotransferrin	30794292	IPI00710664.1	53.1	134	98	0	0	35	33
121	Lethal(3)malignant brain tumor-like protein 4	505792423		2.5	1	1	0	1	2	0
122	Leucine proline-enriched proteoglycan (leprecan) 1	507937306		1.9	1	1	0	1	1	1
123	Lipopolysaccharide-binding protein	84579853	IPI00730056.1	2.3	5	2	0	0	1	1
124	Lipoprotein lipase	115497164	IPI00692291.3	22.0	152	100	99	100	100	99
125	Lymphocyte antigen 96	114051704	IPI00689371.2	6.3	9	3	0	0	1	2
126	Lymphocyte-specific protein 1 isoform X6	587003867		5.8	4	3	0	0	1	2
127	Mammaglobin-A	155372309	IPI00711254.1	14.1	1	10	0	0	7	0
128	Mammary serum amyloid A3.2	347300329	IPI01017597.1	9.2	11	17	1	0	0	13
129	Monocyte differentiation antigen CD14 isoform X1	528956860	IPI00686931.2	22.7	25	82	0	68	47	52
130	Mucin-1	41386778	IPI00706283.1	3.1	13	100	7	8	43	37
131	Mucin-15	41386723	IPI00716220.1	7.3	10	99	100	94	97	98
132	Myristoylated alanine-rich C-kinase substrate	148872484	IPI00760436.1	6.0	6	0	9	0	6	0
133	Neutrophil gelatinase-associated lipocalin isoform X3	528912092	IPI00685784.3	30.5	11	28	95	74	65	66
134	Nucleobindin-1	115497814	IPI00722271.2	28.1	117	100	0	38	48	46
135	Nucleobindin-2	115496067	IPI00696729.2	15.2	73	0	100	0	32	36
136	Olfactory receptor 2S2-like	724801196		2.2	1	0	4	1	2	1
137	Osteopontin isoform X1	528952550	IPI00691887.2	31.7	71	99	100	100	99	100
138	Pancreatic elastase inhibitor	861514		66.7	1	10	0	0	1	6
139	Pancreatic secretory granule membrane major glycoprotein GP2	341572597		23.0	84	100	96	100	100	98
140	Peptidoglycan recognition protein 1	27808640	IPI00701640.1	13.7	5	0	15	63	37	13
141	Peptidyl-prolyl cis-trans isomerase A	47523764	IPI00697285.3	16.5	101	6	2	8	4	6
142	Peptidyl-prolyl cis-trans isomerase B	555965067	IPI00702098.4	6.0	85	31	0	0	14	8
143	Peptidyl-prolyl cis-trans isomerase FKBP1A	78365305	IPI00698916.2	25.0	98	7	0	0	2	2
144	Perilipin-2 isoform X2	528958213	IPI01017444.1	38.0	96	100	100	100	100	100
145	Platelet glycoprotein 4	521258696	IPI00710204.3	15.5	106	100	100	100	100	100
146	Polymeric immunoglobulin receptor	3914346	IPI00696714.1	30.0	28	100	0	100	68	64
147	Polymeric immunoglobulin receptor	296479365		23.9	21	100	100	100	100	100
148	Polyubiquitin	2627129		21.0	380	0	79	0	24	29
149	Prosaposin	27806447	IPI00718311.3	5.0	54	25	0	0	11	6
150	Prostaglandin-H2 D-isomerase	27807521	IPI00709683.1	7.3	6	65	94	100	85	87
151	Protein CREG1	115495283	IPI00702458.2	20.4	11	78	0	13	30	33
152	Protein HP-25 homolog 1	114050753	IPI00724799.2	7.1	3	1	0	0	1	0
153	Protein HP-25 homolog 2	114052108	IPI00700655.3	14.9	3	7	2	40	27	4
154	Protein inturned	617602241		1.3	1	1	0	0	1	0
155	Protein OS-9	77735409	IPI00706896.1	4.5	2	5	0	1	2	2
156	Prothrombin	135806	IPI00710799.1	2.2	7	6	1	0	2	3
157	Ras-related protein Rab-11A	84000297	IPI00695221.3	11.1	82	1	0	0	1	0
158	Ras-related protein Rab-18	115495023	IPI00691826.3	7.3	123	3	0	0	1	2
159	Rhophilin-2-like protein RHPN2P1	190360225		2.4	2	0	1	0	1	0
160	Ribonuclease 4	32363484	IPI00697112.1	9.2	1	0	81	0	30	25
161	Ribonuclease 4	95006989	IPI00760446.1	28.6	4	31	0	3	12	11
162	Ribonuclease pancreatic	133210		10.5	100	0	19	0	3	10
163	Secretoglobin family 1D member	118150406	IPI00824879.1	21.6	4	100	100	100	100	100
164	Selenium-binding protein 1		IPI00718529.1	1.7	1	8	0	3	3	4
165	Selenoprotein	148680082		13.0	69	45	0	9	23	14
166	Serotransferrin	2501351	IPI00690534.1	45.5	61	100	95	100	100	97
167	Serpin A3-1	160332365	IPI00700622.4	12.9	32	100	0	77	67	51
168	Serum albumin	1351907	IPI01028455.1	65.1	40	100	61	100	83	90
169	Sodium-dependent phosphate transport protein 2B	27807195	IPI00703813.1	5.9	7	92	0	0	35	29
170	Sulfhydryl oxidase 1	156120795	IPI00867237.1	19.1	11	98	27	97	75	72
171	Superoxide dismutase	134289051	IPI00847121.1	11.8	73	0	1	0	0	1
172	Sushi repeat-containing protein SRPX	507969850		3.9	3	0	2	6	2	4
173	Tetranectin	114051137	IPI00717369.1	6.9	5	89	0	1	34	29
174	Transforming protein RhoA	10835049	IPI00688998.3	6.2	49	0	0	1	1	0
175	Transthyretin	27806789	IPI00689362.1	34.7	24	0	91	77	59	50
176	Uncharacterized proteinb (P02666 Beta-casein 71% ident.)		IPI00712994.3	33.5	5	18	0	0	7	6
177	Uncharacterized proteinb (F1MGU7 Fibrinogen gamma-B chain 100% ident.)		IPI00843209.1	17.2	16	99	0	0	35	34
178	Uncharacterized proteinb (A5PK72 Uncharacterized protein 92% ident.)		IPI01017618.1	20.6	10	42	0	0	10	20
179	Uncharacterized proteinb (A0A0A0MP92 Serpin A3-7 98% ident.)		IPI00971595.1	21.1	4	1	0	6	5	0
180	Uncharacterized proteinb (Q2HJI6 Granulin 99% ident.)		IPI00904166.1	6.3	99	98	0	41	57	37
181	Uncharacterized proteinb (F1MLW7 Uncharacterized protein 97% ident.)		IPI00838162.2	20.9	1	0	100	0	32	36
182	Uncharacterized protein LOC524810b (A5D7Q2 Uncharacterized protein 100% ident.)	326937675	IPI00852509.1	10.9	6	100	100	100	100	100
183	Vitamin D-binding protein	78369364	IPI00823795.1	8.0	20	38	0	0	21	6
184	Xanthine dehydrogenase/oxidase	296482686		15.6	16	0	100	0	32	36
185	Xanthine dehydrogenase/oxidase	109940048	IPI00695367.3	14.1	16	100	0	100	68	64
186	Zinc-alpha-2-glycoprotein	77735615	IPI00698993.1	11.4	2	1	100	100	64	67

Proteins whose occurrence varies more than 10% across breeds are highlighted in bold.

^aOccurrence is defined as the ratio of the number of samples in which the protein was identified over the total number of samples in the method or breed expressed in percent.

^bAmino acid sequence of uncharacterized proteins were blasted against uniprot database. Best hit is indicated in brackets with the percentage of identity.