Extended Data Table 1.

a.–c. 20 µg of native cell membrane proteins were incubated with 50 µg of syngeneic (C57Bl/6) or allogeneic (129S1) IgG coupled to protein G magnetic beads and precipitated proteins were analyzed by mass-spectrometry. Tables show the conversion to Spectral Abundance Factor (SAF) and subsequent Normalized Spectral Abundance Factor (NSAF). This was based on the equation: NSAF = (SpC/MW)/Σ(SpC/MW)N. Where SpC = Spectral Counts, MW = Protein MW in kDa and N = Total Number of Proteins.

a. Proteins enriched by alloIgG
Identified Proteins		Accession Number	C57 SpC	129 SpC	C57 SAF	129 SAF	C57 NSAF	129 NSAF	C57/129 ratio
Endoplasmic reticulum membrane
1	Transmembrane protein 93	sp|Q9CQW0|TMM93_MOUSE	0	2	0	0.166667	0	0.0007367	2
2	Endoplasmic reticulum-Golgi intermediate compartment protein 3	sp|Q9CQE7|ERGI3_MOUSE	0	2	0	0.046512	0	0.00020559	2
3	Reticulon-4	sp|Q99P72|RTN4_MOUSE	0	2	0	0.015748	0	6.9609E-05	2
4	Uncharacterized protein C12orf41 homolog	sp|Q8BQR4|CL041_MOUSE	0	2	0	0.037037	0	0.00016371	2
5	Erlin-2	sp|Q8BFZ9|ERLN2_MOUSE	0	2	0	0.052632	0	0.00023264	2
6	Transitional endoplasmic reticulum ATPase	sp|Q01853|TERA_MOUSE	0	2	0	0.022472	0	9.933E-05	2
7	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1	sp|P61804|DAD1_MOUSE	0	2	0	0.166667	0	0.0007367	2
8	Calnexin	sp|P35564|CALX_MOUSE	0	2	0	0.029851	0	0.00013195	2
9	Calumenin	sp|O35887|CALU_MOUSE	0	2	0	0.054054	0	0.00023893	2
10	Vesicle-associated membrane protein-associated protein A	sp|Q9WV55|VAPA_MOUSE	0	3	0	0.107143	0	0.00047359	3
11	Mannosyi-oligosaccharide glucosidase	sp|Q80UM7|MOGS_MOUSE	0	3	0	0.032609	0	0.00014414	3
12	Neutral alpha-glucosidase	sp|Q8BHN3|GANAB_MOUSE	0	3	0	0.028037	0	0.00012393	3
13	ERO1-like protein alpha	sp|Q8R180|ERO1A_MOUSE	0	5	0	0.092593	0	0.00040928	5
14	UDP-glucose:glycoprotein glucosyltransferase 1	sp|Q6P5E4|UGGG1_MOUSE	0	5	0	0.028409	0	0.00012557	5
15	Prolyl 4-hydroxylase subunit alpha-1	sp|Q60715|P4HA1_MOUSE	0	5	0	0.081967	0	0.00036231	5
16	Epoxide hydrolase 1	sp|Q9D379|HYEP_MOUSE	0	9	0	0.169811	0	0.0007506	9
17	Calreticulin	sp|P14211|CALR_MOUSE	0	14	0	0.291667	0	0.00128922	14
18	Sarcoplasmic/endoplasmic reticulum calcium ATPase	sp|O55143|AT2A2_MOUSE	8	18	0.06956522	0.156522	0.0003684	0.00069185	1.8782025
19	Protein disulfide-isomerase A4	sp|P08003|PDIA4_MOUSE	0	12	0	0.166667	0	0.0007367	12
20	Protein disulfide-isomerase	sp|P09103|PDIA1_MOUSE	0	12	0	0.210526	0	0.00093056	12
21	Protein disulfide-isomerase A3	sp|P27773|PDIA3_MOUSE	0	9	0	0.157895	0	0.00069792	9
22	Protein disulfide-isomerase A6	sp|Q922R8|PDIA6_MOUSE	0	11	0	0.229167	0	0.00101296	11
Melanosomes and vesicles membranes
1	Peptidyl-prolyl cis-trans isomerase B	sp|P24369|PPIB_MOUSE	0	7	0	0.291667	0	0.00128922	7
Cell membrane
1	T-complex protein 1 subunit gamma	sp|P80318|TCPG_MOUSE	0	2	0	0.032787	0	0.00014492	2
2	Monocarboxylate transporter 4	sp|P57787|MOT4_MOUSE	0	2	0	0.04	0	0.00017681	2
3	Nicastrin	sp|P57716|NICA_MOUSE	0	2	0	0.025641	0	0.00011334	2
4	Basigin	sp|P18572|BASI_MOUSE	0	2	0	0.047619	0	0.00021048	2
5	Vesicle-associated membrane protein-associated protein A	sp|Q9WV55|VAPA_MOUSE	0	3	0	0.107143	0	0.00047359	3
6	Retrovirus-related Env polyprotein from Fv-4	sp|P11370|ENV2_MOUSE	0	3	0	0.040541	0	0.0001792	3
7	Synaptic vesicle membrane protein	sp|Q62465|VAT1_MOUSE	0	4	0	0.093023	0	0.00041118	4
8	4F2 cell-surface antigen heavy chain	sp|P10852|4F2_MOUSE	0	4	0	0.068966	0	0.00030484	4
9	Alpha-enolase	sp|P17182|ENOA_MOUSE	0	5	0	0.106383	0	0.00047023	5
10	Integrin-linked protein kinase	sp|O55222|ILK_MOUSE	0	4	0	0.078431	0	0.00034668	4
11	Transmembrane glycoprotein NMB	sp|Q99P91|GPNMB_MOUSE	2	15	0.03125	0.234375	0.0001655	0.00103598	6.2606749
12	MLV-related proviral Env polyprotein	sp|P10404|ENV1_MOUSE	0	13	0	0.185714	0	0.00082089	13
13	ERO1-like protein alpha	sp|Q8R180|ERO1A_MOUSE	0	5	0	0.092593	0	0.00040928	5
14	Clathrin heavy chain 1	sp|Q68FD5|CLH_MOUSE	0	5	0	0.026042	0	0.00011511	5
15	Desmoglein-1-alpha	sp|Q61495|DSG1A_MOUSE	2	5	0.0173913	0.043478	9.209E-05	0.00019218	2.0868916
16	Sodium/potassium-transporting ATPase subunit alpha-1	sp|Q8VDN2|AT1A1_MOUSE	4	12	0.03539823	0.106195	0.0001874	0.0004694	2.50427

b. Proteins equally enriched by synIgG and alloIgG
Identified Proteins		Accession Number	C57 SpC	129 SpC	C57 SAF	129 SAF	C57 NSAF	129 NSAF	C57/129 ratio
Endoplasmic reticulum membrane
1	DnaJ homolog subfamily B member 11	sp|Q99KV1|DJB11_MOUSE	8	6	0.19512195	0.146341	0.0010332	0.00064686	0.6260675
2	78 kDa glucose-regulated protein	sp|P20029|GRP78_MOUSE	73	71	1.01388889	0.986111	0.0053687	0.00435879	0.8118866
3	Serpin H1	sp|P19324|SERPH_MOUSE	11	17	0.23404255	0.361702	0.0012393	0.00159879	1 2900785
4	Protein transport protein Sec61 subunit beta	sp|Q9CQS8|SC61B_MOUSE	2	3	0.2	0.3	0.001059	0.00132605	1.252135
5	Leucine-rich repeat-containing protein 59	sp|Q922Q8|LRC59_MOUSE	3	2	0.08571429	0.057143	0.0004539	0.00025258	0.5565044
6	Protein transport protein Sec61 subunit alpha isoform 1	sp|P61620|S61A1_MOUSE	9	10	0.17307692	0.192308	0.0009165	0.00085003	0.9275074
7	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit	sp|O54734|OST48_MOUSE	3	5	0.06122449	0.102041	0.0003242	0.00045104	1.3912611
8	Estradiol 17-beta-dehydrogenase 12	sp|O70503|DHB12_MOUSE	7	6	0.2	0.171429	0.001059	0.00075774	0.7155057
Melanosomes and vesicles membranes
1	Flotillin-2	sp|Q60634|FLOT2_MOUSE	3	2	0.06382979	0.042553	0.000338	0.00018809	0.5565044
2	Cathepsin D	sp|P18242|CATD_MOUSE	3	5	0.06666667	0.111111	0.000353	0.00049113	1.3912611
3	AP-2 complex subunit beta	sp|Q9DBG3|AP2B1_MOUSE	8	5	0.07619048	0.047619	0.0004034	0.00021048	0.5217229
4	AP-2 complex subunit mu	sp|P84091|AP2M1_MOUSE	4	5	0.08	0.1	0.0004236	0.00044202	1.0434458
5	Annexin A2	sp|P07356|ANXA2_MOUSE	4	6	0.1025641	0.153846	0.0005431	0.00068003	1.252135
6	Melanocyte protein PMEL	sp|Q60696|PMEL_MOUSE	5	4	0.07575758	0.060606	0.0004011	0.00026789	0.6678053
Cell membrane
1	Desmoplakin	sp|E9Q557|DESP_MOUSE	63	60	0.18918919	0.18018	0.0010018	0.00079643	0.7950063
2	PDZ domain	sp|Q9Z0G0|GIPC1_MOUSE	13	9	0.36111111	0.25	0.0019121	0.00110504	0.5779085
3	Junction plakoglobin	sp|Q02257|PLAK_MOUSE	37	49	0.45121951	0.597561	0.0023893	0.00264133	1.1054885

c. Proteins enriched by synIgG
Identified Proteins		Accession Number	C57 SpC	129 SpC	C57 SAF	129 SAF	C57 NSAF	129 NSAF	C57/129 ratio
Endoplasmic reticulum membrane
1	Stromal cell-derived factor 2-like protein 1	sp|Q9ESP1|SDF2L_MOUSE	3	0	0.125	0	0.0006619	0	3
2	Nicalin	sp|Q8VCM8|NCLN_MOUSE	2	0	0.03174603	0	0.0001681	0	2
3	Translocation protein SEC62	sp|Q8BU14|SEC62_MOUSE	4	0	0.08695652	0	0.0004604	0	4
4	Disco-interacting protein 2 homolog B	sp|Q3UH60|DIP2B_MOUSE	4	0	0.02339181	0	0.0001239	0	4
melanosomes and Vesicles membranes
1	Vacuolar protein sorting-associated protein 35	sp|Q9EQH3|VPS35_MOUSE	2	0	0.02173913	0	0.0001151	0	2
2	Angiomotin-like protein 2	sp|Q8K371|AMOL2_MOUSE	6	0	0.07058824	0	0.0003738	0	6
3	Fibrous sheath-interacting protein 2	sp|A2ARZ3|FSIP2_MOUSE	9	0	0.01146497	0	6.071E-05	0	9
Cell membrane