Table 1. List of mouse and rat proteomics datasets that were reanalysed.

Expression Atlas accession numbers	PRIDE dataset identifiers	Tissues	Organs	Species	Strains	Fractionation	Number of MS runs	Number of samples	Number of protein groups†	Number of peptides†	Number of unique peptides†	Number of unique genes mapped†
E-PROT-7§	PXD000867 [18]	Liver	Liver	Mus musculus	C57BL/6J	Yes	24	4	12,792	246,738	167,725	9,715
E-PROT-10§	PXD000288 [19]	Triceps muscles	Triceps Muscles	Mus musculus	C57BL/6	Yes	36	3	10,870	189,553	126,670	6,421
E-PROT-16	PXD003155 [20]	Cerebellum, Liver	Brain, Liver	Mus musculus	C57BL/6	No	24	12	4,508	59,696	45,728	3,797
E-PROT-74	PXD004612 [21]	Achilles and Plantaris tendon	Tendon	Mus musculus	C57BL/6	No	8	8	457	6,643	3,271	273
E-PROT-75	PXD005230 [22]	Hippocampus, Cerebellum, Cortex	Brain	Mus musculus	C57BL/10J	Yes	72	36	7,663	63,479	41,683	6,037
E-PROT-76	PXD009909 [23]	Retina	Eye	Mus musculus	ND4 Swiss Webster	Yes	12	1	5,002	29,454	24,961	3,686
E-PROT-77	PXD012307 [24]	Lung	Lung	Mus musculus	C57BL/6	No	32	2	6,809	106,391	73,950	5,795
E-PROT-78	PXD009639 [25]	Lens	Eye	Mus musculus	CD1	Yes	10	1	4,519	20,779	18,006	3,064
E-PROT-79	PXD019394 [26]	Heart, Kidney, Liver, Lung, Brain, Spleen, Testis, Pancreas	Heart, Kidney, Liver, Lung, Brain, Spleen, Testis, Pancreas	Mus musculus	Swiss-Webster	Yes	96	8	9,853	141,506	105,701	8,185
E-PROT-81	PXD012636 [27]	Left atrium, Left ventricle, Right atrium, Right ventricle	Heart	Mus musculus	C57BL/6	Yes	120	4	7,772	146,966	99,577	6,435
E-PROT-82	PXD019431 [28]	Articular cartilage	Articular cartilage	Mus musculus	BALB\_c	No	72	6	1,815	17,695	15,191	1,518
E-PROT-83	PXD022614 [29]	Brain	Brain	Mus musculus	C57BL/6J:Rj C57BL/6JRccHsd	Yes	120	6	6,645	97,443	69,884	5,673
E-PROT-84	PXD004496 [30]	Hippocampus	Brain	Mus musculus	C57BL/6J	Yes	204	17	4,192	37,363	30,100	3,424
E-PROT-85	PXD008736 [31]	Right atrium, Sinus node	Heart	Mus musculus	C57BL/6J	Yes	143	6	7,906	144,926	94,379	6,554
E-PROT-86§	PXD012677 [32]	Amygdala	Brain	Rattus norvegicus	Sprague Dawley	No	3	3	1,872	15,326	12,367	1,382
E-PROT-87§	PXD006692 [33]	Lung	Lung	Rattus norvegicus	Sprague Dawley	No	10	10	2,079	14,440	11,696	1,398
E-PROT-88§	PXD016793 [34]	Liver	Liver	Rattus norvegicus	Sprague Dawley	No	8	8	4,787	57,998	46,411	3,743
E-PROT-89§	PXD004364 [35]	Testis	Testis	Rattus norvegicus	Sprague Dawley	No	3	3	2,351	15,880	13,674	1,601
E-PROT-91	PXD001839 [36]	Left ventricle	Heart	Rattus norvegicus	F344/BN	No	12	12	1,345	10,310	8,804	925
E-PROT-92§	PXD013543 [37]	Left ventricle	Heart	Rattus norvegicus	Wistar	No	8	8	1,858	17,303	13,622	1,340
E-PROT-93	PXD016958 [38]	First segment of proximal tubule, second segment of proximal tubule, third segment of proximal tubule, medullary thick ascending limb, cortical thick ascending limb, distal convoluted tubule, connecting tubule, cortical collecting duct, outer medullary collecting duct, inner medullary collecting duct	Kidney	Rattus norvegicus	Sprague Dawley	Yes	132	32	7,846	103,886	83,662	6,130
E-PROT-94	PXD003375 [39]	Caudal and rostral segments of spinal cord	Spinal cord	Rattus norvegicus	Wistar	Yes	21	18	2,477	29,213	22,025	1,926
E-PROT-95§	PXD015928 [40]	Tendon	Tendon	Rattus norvegicus	Wistar	No	3	3	199	1,253	1,063	101
TOTAL	23 datasets (Mouse: 14, Rat: 9)	34 tissues (Mouse: 21, Rat: 18)	14 organs (Mouse: 12, Rat: 8)				1,173 MS runs (Mouse: 973, Rat: 200)	211 samples (Mouse: 114, Rat: 97)

^§Only normal/untreated samples within this dataset are reported in this study. However, results from both normal and disease samples are available in Expression Atlas

^† Numbers after post-processing.