Table I Top most overexpressed MIPs in WT relative to dKO DCs

No.	m/z	Charge	Mascot score	MHC I allele	Peptide sequence	Gene ID	Gene symbol	Gene Name	WT/dKO ratio
1	520.22	2	66	H2D^b	GGVVNMYHM	16913	Psmb8	Proteasome subunit, beta type 8 (LMP7)	≥1181,3
2	460.25	2	40	H2K^b	ATRSFPQL	11750	Anxa7	Annexin A7	≥380,8
3	624.83	2	44	H2D^b	HAIRNSFQYL	170749	Mtmr4	Myotubularin related protein 4	≥207,3
4	472.28	2	55	H2K^b	TIIIFHSL	14050	Eya3	Eyes absent 3 homolog (Dm)	160,5
5	497.27	2	43	H2K^b	VVYIYHSL	67014	Mina	Myc induced nuclear antigen	≥159,3
6	467.28	2	47	H2K^b	SALRFLNL	71728	Stk11ip	Ser/Thr kinase 11 interacting protein	120,8
7	479.28	2	39	H2K^b	KNVLFSHL	19084	Prkar1a	Protein kinase, cAMP dependent regulatory, type I, alpha	≥109,8
8	524.27	2	65	H2D^b	RQILNADAM	66185	1110037F02Rik	RIKEN cDNA 1110037F02 gene	≥96,8
9	496.78	2	42	H2D^b	SGLLNMTKI	216445	Arhgap9	Rho GTPase activating protein 9	≥93,9
10	525.26	2	29	H2K^b	HVYYFAHL	74558	Gvin1	GTPase, very large interferon inducible 1	≥93,4
11	510.80	2	56	H2K^b	VITNFSARI	68505	1110014N23Rik	RIKEN cDNA 1110014N23 gene	≥83,3
12	507.26	2	49	H2K^b	STLIYRNM	75660	Lin37	Lin-37 homolog (C. elegans)	≥82,1
13	597.28	2	27	H2D^b	SAIHNFYDNI	68652	Map3k7ip2	MAPKKK 7 interacting protein 2	≥80,5
14	523.75	2	34	H2D^b	SQVYNDAHI	66923	Pbrm1	Polybromo 1	≥76,9
15	537.27	2	40	H2K^b	LVYQFKEM	56501	Elf4	E74-like factor 4 (ets domain transcription factor)	≥76,2
16	461.76	2	62	H2D^b	GAVQNIAHL	74125	Armc8	Armadillo repeat containing 8	68,5
17	496.28	2	32	H2K^b	ISLEFRNL	14137	Fdft1	Farnesyl diphosphate farnesyl transferase 1	68,1
18	506.30	2	43	H2K^b	KSYLFQLL	12566	Cdk2	Cyclin-dependent kinase 2	≥66,4
19	447.74	2	53	H2D^b	GGIQNVGHI	23918	Impdh2	Inosine 5′-phosphate dehydrogenase 2	54,8
20	493.24	2	41	H2K^b	SNYRFEGL	319955	Ercc6	Excision repair cross-complementing rodent repair deficiency, complementation group 6	≥46,4
21	479.75	2	37	Qa2	GLMTTVHAI	640374	LOC640374	Similar to GAPDH	42,0
22	645.34	2	33	H2D^b	AQYGNILKHVM	69482	Nup35	Nucleoporin 35	≥40,3
23	486.78	2	48	H2D^b	KAPLNIAVM	667214	RP23–269N23.3	Similar to immunity-related GTPase family, cinema 1	39,8
24	510.81	2	54	H2D^b	YGLLNVTKI	75415	Arhgap12	Rho GTPase activating protein 12	≥37,6
25	501.27	2	42	H2D^b	SALANYIHL	58245	Gpr180	G protein-coupled receptor 180	≥37,4

MIPs that were not detected on dKO cells were attributed the intensity value 15,000, which represents the threshold for limit of detection. Ratios with the symbol ≥ indicate peptides for which the exact fold change could not be measured because they were detected only in WT DCs. See supplemental Table S1 for a complete list of MIPs detected on DCs.