Table 1. List of Pig Proteomics Datasets and Their Main Characteristics.

expression Atlas accession number	proteomics data set identifier*	breed	tissues	organs	mass spectrometer	number of MS runs	number of samples	fraction	number of protein groups†	number of peptides†	number of unique peptides†	number of unique genes (canonical proteins) mapped†
E-PROT-111	PXD00180027	landrace	retina	eye	Q exactive Plus	48	16	yes	4579	36,992	28,055	3643
E-PROT-113	PXD00291828	NA	biceps femoris	muscle	LTQ orbitrap XL	6	6	no	1272	9148	6163	841
E-PROT-114	PXD00320429	landrace	bile duct, heart, spleen, lung, brain, liver, diaphragm, pancreas, kidney	biliary system, heart, spleen, lung, brain, liver, diaphragm, pancreas, kidney	LTQ orbitrap Elite	108	9	Yes	5969	85,655	57,338	5065
E-PROT-115	PXD00957730	NA	heart	heart	Q exactive HF	30	6	yes	4258	47,975	32,956	3582
E-PROT-117	PXD01136031	landrace × piétrain	cecum, colon, Ileum, Jejunum	intestine	Q exactive Plus	16	16	no	4716	55,392	41,184	3981
E-PROT-118	PXD01153632	NA	liver	liver	Q exactive HF-X	5	5	no	2356	18,816	15,078	1773
E-PROT-119	PXD01175533	House swine	eye	eye	LTQ orbitrap XL	204	12	yes	1337	7039	5660	888
E-PROT-120	PXD01263634	NA	heart	heart	Q exactive HF	120	4	yes	7747	151,177	94,341	6982
E-PROT-122	PXD01489335	NA	biceps femoris, triceps muscles	muscle	Q exactive HF-X	8	4	yes	1287	13,065	8527	1004
E-PROT-124	PXD01600336	NA	biceps femoris, triceps muscles	muscle	Q exactive HF-X	8	4	yes	2379	22,409	15,650	1885
E-PROT-125	PXD01767137	NA	liver	liver	Q exactive HF-X	8	8	no	3128	32,215	24,585	2576
E-PROT-126	PXD01985238	NA	heart	heart	Q exactive HF-X	8	8	no	1527	13,511	10,085	1143
E-PROT-130	PXD02691039	NA	subcutaneous adipose tissue, mesenteric adipose tissue	adipose tissue	Q exactive HF	10	10	No	2586	23,718	17,676	2107
E-PROT-131	PXD02777240	landrace × swabian-hall	skeletal muscle, heart	skeletal muscle, heart	Q exactive HF	20	20	no	3242	39,140	25,993	2797
TOTAL	14 data sets		20 tissues	14 organs		599 MS runs	128 samples