Supplementary Table 1: Ligands of HLA-B*44:09 Derived from LCL 721.221 Cells

Supplementary Table 1: Ligands of HLA-B*44:09 derived from LCL 721.221 cells

Peptide position

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

A R Q V E L LADAM metallopeptidase with thrombospondin type 1

N E P N E L Lcytidine monophosphate-N-acetylneuraminic hydroxylase

L E A N F E K IATPase, H+ transporting, lysosomal V0 subunit a 1

S I L N Y L K Lglutamate-cysteine ligase, catalytic subunit

V D I L P F L LC8orf30A prot.

A E E E G L R Lfamily with sequence similarity 102, member B

S S F V L P K LRas and Rab interactor 2

M R D M A Q L RSMG5 prot.

V E R C M V R KKIAA0226

W L D H Q Q V Lunnamed prot. product (homo sapiens)

S S L H Q D N Lzinc finger and BTB domain containing 7B

K S F K L S G Fmyristoylated alanine-rich prot. kinase C substrate

G G L R A E L LNuMA prot. (Homo sapiens)

V G Y R V A T Fdolichol-phosphate-mannose synthase (Homo sapiens)

A A A Y L Q H LGT24 (Homo sapiens)

K S F P I S H Vgap junction prot., α 1, 43kDa

F E Q F K E V Linositol polyphosphate-4-phosphatase, type I

K S Y L M N K Lguanylate binding protein 1, interferon-inducible

G G L R A E L Lnuclear mitotic apparatus prot. 1, isof. CRA_c

Q A A I A E L LDEP domain containing 1

L E E Q I A K Vkinetochore associated prot. 2

N P D A V A L Ldynein, axonemal, heavy chain 12

G G L R A E L Lnuclear mitotic apparatus prot. 1

K S Y L M N R Lguanylate binding prot. 4

V F N D G F R Lcyritestin 2

W R S L H L V IKIAA1219

N P V S G I L Isolute carrier family 14 (urea transporter)

L G G R L S I Ptransmembrane receptor UNC5H2

T R F F D I Q Lmammalian ependymin related prot. 1

E E A N L M K T LIsof. LYN A of Tyrosine-prot. kinase

A E A F L L R L YPutative uncharacterized prot. ERCC4

Y E M E V S Q R LLONP2 protease homolog

V T L G T R G V YProt. tyrosine phosphatase, receptor type, T

A E A L A Q R T Y12 kDa prot.

A E A L P K Q S VBTF3 Isof. 2 of Transcription factor BTF3

S E L E K T F G WIsof. LYSp100-A of Nuclear body prot. SP140

E E Q V A R E S YOTU domain containing 5 isof. c

S E E D L K V L FIsof. 1 of Polypyrimidine tract-binding prot. 1

S E S N F A R A Y16 kDa prot.

A E A F L V H L FIsof. 2 of Histone H3-like centromeric prot. A

M E S D F E Q K LIsof. 2 of Prot. diaphanous homolog 1

S E Q P A K A T FNuclear pore complex prot. Nup153

Q E V G Y T I R FATP-dependent RNA helicase DHX8

A E M L R S I S FCleavage stimulation factor 50 kDa subunit

A E F K E A F S LPutative uncharacterized prot. CALM2

A E N G M Y I R MPutative uncharacterized prot. CAD

A E I L M K T L LProbable E3 ubiquitin-prot. ligase HERC1

T E L E Y I H A LExocyst complex component 4

M E G L T A K V FDNA topoisomerase 1

A E G D L I E H FHeterogeneous nuclear ribonucleoprot. A0

Q E F L T K L A FCentromere prot. F

E E A G G R P A McDNA FLJ54020, nuclear ribonucleoprot.

G L L G L P G A Lsolute carrier family 23 (nucleobase transporters)

L E Q M L Q Q A LZCPW2_HUM Zinc finger CW-type PWWP dom.prot. 2

L E M I E P R T Lribosomal prot. S16

G G D F K I P V LKIAA0556 prot.

I A G V I A G I Lprot. tyrosine phosphatase, receptor type, M

S T D E T S Q I VPPFIA2 prot.

S E S P I V V V LSEC11-like 1 signal peptidase 18kDa

E E L P H I H A FBOLA2_HUMAN BolA-like prot. 2

A E F E L P K T MIGBP1_HUMAN Immunoglobulin-binding prot. 1

K E S T L H L V Lsimilar to ubiquitin prot.

A E G L L Q E A Lcoatomer prot. complex, subunit epsilon

L E K D L E E I LCCAR1_HUMAN Cell div. cycle and apoptosis regulator

A E I E D I R V LPLEK_HUMAN Pleckstrin (Platelet p47 prot.)

Q E I P V N V R FCNDP2_HUMAN Cytosolic non-specific dipeptidase

S E T L K H L V Lnuclear RNA export factor 5

G I S F Q I Y V LHUMAN Cullin 2 [CUL2]

L E I V F R V G Lecotropic viral integration site 5-like, isof. CRA_b

N E I V T I E R Lfragile X mental retardation 1, isof. CRA_e

G S V L G G L L Lintegrin, alpha 10

G L R H A K E V Lzinc finger CCCH-type containing 18

Q L Q Q A K E V Ihypothetical prot.LOC347475

Q F P M G P A C Icalcium binding prot. 5

T E H A Q L V Q Iperoxisome proliferator activated receptor

R S L P E P A Q RKIAA0301

P E L V L E R A Lprotocadherin gamma subfamily A, 3

A E N I S R V L Yunnamed prot. product (Homo sapiens)

Q E S N V R L K Lseptin 11

A R F P S T P G Pmyel./lymph., mix.-lineage leukemia 2, isoform CRA_b

Q T R P Y G F G Lsolute carrier fam. 30 (zinc transporter), member 6

S E Y A R P H V Matrophin-1 (Homo sapiens)

A E K L I T Q T FNUDC 24 kDa prot.

V E K V P N P S Lsimilar to BC003940 prot.

T S S Y K I P S Vfurry-like (Homo sapiens)

E E A E I I R K Ypoly (ADP-ribose) polymerase family, member 1,

G G L V S L G L PKIAA1619 prot. (Homo sapiens)

D P Q S P M A G Lputative prot. O-mannosyltransferase (Homo sapiens)

A E S I V V H T YFLJ54022, highly similar to Exportin-2

E E V K S F R V LETNK1 prot.

S E P N P R P V Fcarbamoyl-phosphate synthetase 2

M R A Q D P G V M KIAA1318 prot. (Homo sapiens)

R E A P E R P S Lnon-SMC element 4 homolog A

A E I D S I H Q Lgrowth-inhibiting prot. 9

E E I D H A V H Lmethionyl aminopeptidase 1, isoform CRA_a

Q E H P S I R T Limportin 5

E I D V I Q E V LMDN1, midasin homolog

A E Q M R K I A Lsequestosome 1, isof. CRA_a

A Q R P N L I G LRNA binding motif prot. 26

A E M A M K V E Lacyl-Coenzyme A dehydrogenase

A E R P Q E W A Mnucl. fact. of kappa light polypeptide gene enhancer

P S T W A H I V LNDC80 prot.

S E S N F S P K Fnudix -type motif 9 isof. b

F F V S A K E V Lmitofusin 1

A T D W L G S I Venhancer of mRNA decapping 3

T R T S R H I V LBMAL1e

E T P P P D A L Ehypothetical prot. LOC118461 isof. 1

G G P G G L Q P LV-set and transmembrane dom. containing 2 like prot.

A E K V E I A T Lproteasome (prosome, macropain) subunit, α type, 4

T V A S E M N R IDDHD domain containing 2, isof. CRA_a

Q E V A V R V E LFGF receptor activating prot. 1

K N E Q E R V L FPotassium voltage-gated channel, subfam. G, member 1

I S F F Q V D G Ltelomerase-associated prot. 1

A E M Q W K R D YNADH dehydrogenase (ubiquinone) 1 β subcomplex

W V L G M V D G Lolfactory receptor, family 2, subfamily T, member 34

V P G P H M V E Runnamed prot. product (homo sapiens)

E G K I H S L V Ltitin, isof. CRA_a

S E I E A K V R YTalin-1

H E A Q I N N M E MImportin subunit alpha-1

A E I S D V W E E MIsof. 2 of Spectrin beta chain, brain 1

S E I L Q K E V Y LcDNA FLJ50448, Vacuolar prot.

A E Q I Q K V N E MIsof. 2 of 12 chromosomal region 1 prot

N E I E D T F R Q FATPase, lysosomal 14kDa, V1 subunit F

E E M D L K V L Q FIsof. 3 of E3 ubiquitin-prot. ligase BRE1B

S E M D V T G Q A FIsof. 3 of E3 ubiquitin-prot. ligase BRE1B

N E D E P I R V S YOTU domain containing 5 isof. c

A E I A E S V Q A FAlpha- and gamma-adaptin-bind. prot. p34

Q E S E V L E R Q MIsof. of Nucl. body prot. SP140

E E A A V A I K A MEIF5A Eukaryotic transl. initiation factor 5A-1-like

N E M E A P T T A YFLJ59379, similar to Hematopoietic lin. cell-specific

A E A E A A S V R M Flotillin 1

A E E S A I R V G FProt. transport prot. Sec24C

A E N P H S E Y G LProt. dpy-30 homolog

A E Q A E R Y D D MYWHAQ 14-3-3 prot. theta

A E L E S S K E Q FGTP-GDP dissociation stimulator 1 isof. 4

M E Q I S I I E R FBruton agammaglobulinemia tyros. kinase, isof. CRA_b

Q E Q A A W Y H T LcDNA FLJ46206 fis, clone TESTI4010721

S E Q P F L L V T YIsof. 2 of Dehydrogenase/reductase SDR fam. member 7

M E M L E A P H Q LPutative uncharacterized prot. RXRB

A E K D S L D P S FIsof. 3 of KH domain

A E A A G L H K V FTopoisomerase II beta

A E M I T G K T L FMitogen-activated prot. kinase 12

Q E T S F T K E A YTPT1-like prot.

I E G A N Q L L E Lmagnesium-dependent phosphatase 1, isof. CRA_c

M E L K S T N I S FCGI-107 prot.

H A V T R A T K M Lubiquitin specific peptidase 24

A E I R H V L V T Lunknown prot. source (homo sapiens)

A E D P L G A I H LPLEK_HUMAN Pleckstrin (Platelet p47 prot.)

A E I D A H L V A LPSA6_HUMAN Proteasome subunit α type-6

S E M H V P S V A LPhosphoinositide-3-kinase, catalytic

S E L P I V T P A LIMA2_HUMAN Importin subunit α-2

F L A G G L H L V Ptransmembrane prot. 105

S E I G G I T I A Hactivator of transcription 6, interleukin-4 induced

L A S S L S H L L Vadenylate cyclase 4, isof. CRA_b

R L G L L S L P G Lhypothetical protein LOC100133143

A E V A A T E I K Mheterogeneous nucl. Ribonucleoprot. M isof. a

N E M Q P N G K V FIsof. Long of Long-chain-fatty-acid--CoA ligase 4

T E M E S M K T T LCoiled-coil domain-containing prot. 99

A E K A P T N I V Yreplication prot. A2, 32kDa

A E M A Q N A V R L46 kDa prot.

R E A N F T V S S MKIAA0111

A E A G S R M D K Lcatenin (cadherin-associated prot.), α 1

E E L S L E G N P Fleucine-rich repeats and WD repeat dom. containing 1

L E G S C L E V T LRNA binding motif prot. 47 isof. b

P A H E V G L V S Lcalmodulin binding transcription activator 2

L E N P G T S P A Lintegrin, α 2 (CD49B, α 2 subunit of VLA-2 receptor),

T T S N N T A T V IPOU class 2 homeobox 1

S E V D L T R S F S FGMP reductase 2

E E M D F P Q L M K MEukaryotic translation initiation factor 3, subunit D

S E Q D W S A I Q N FADP-ribosylation factor-binding prot. GGA2

A E A S A L Y G R A LcDNA FLJ26027 fis, clone PNC04328

N E I D M S N I Q E McDNA 5-PRIME end of clone CS0DJ009YL13 of T cells

M E V N S G I Y R V LHeat shock 70 kDa prot. 14

V T Q I G G G A E S LIsof. 1 of Vacuolar prot. sorting-associate

S E F L Y D K A L T FPutative uncharacterized prot. DHX57

A E I D A S N I V S LNPAT prot.

A E I G A A A Q Q S LIsof. 2 of CDK5 regul. subunit-associated prot. 3

T E M L P S I L N Q LBTF3 Isof. 2 of Transcription factor BTF3

A E I Q N V E G Q N LIsof. LYSp100-A of Nuclear body prot. SP140

K E M F P I E A G A IIsof. 2 of Neutrophil cytosol fact. 1

A E M D K V K E E A MPutative uncharacterized prot. SPATS2L

A E A D S K L K Q V YMetastasis-associated prot. MTA2

E E M E T D A R S S LPutative uncharacterized prot. DKFZp781L0540

A E M P D S A A A L LIsof. of Non-syndromic hearing impairment prot. 5

S E Y S M P S T H A M Sphingosine-1-phosphate phosphatase 1

G E K F E D E N F I LcDNA FLJ75025, Homo sapiens peptidylprolyl isomerase

A E L D P S I A V G FcDNA FLJ41431 fis, clone BRHIP2005932

Q E N P N M R L S Q LCoiled-coil domain-containing prot. 124

G E I D P A T G M V M6-pyruvoyl tetrahydrobiopterin synthaseAEAPSESKPAA

A E A P S E S K P A APhosphatidate phosphatase LPIN2

Q E M N Y I Q K T L FIsof. Short of Long-chain-fatty-acid-CoA ligase 4

S E I K I S N P T E FNUSAP_HUMAN Nucl. and spindle-associated prot. 1

T E M D S H E E K V FHypothetical prot. DKFZp686M09245

A Q A S V E N A A E Eleucine rich repeat containing 37, member A2

S E I E D S T K Q V Fbreast and ovarian cancer susceptibility prot. 2

S L G I G L G M A I Volfactory receptor, family 10, subfamily J, member 3

V G S I L L V G L A Lintegrin, beta 5

A E M G T R T F S A FPutative uncharacterized prot. UGGT2

A E Q Q I T E V F V LIsof. Short of Antigen KI-67

P G D K G E G G A P G Lcollagen, type III, α 1

A E M V V P R S S N V L32 kDa prot.

A E N D I K E S S A V FBRCA1 IRIS

Q E Q F N S I A A H V LcDNA FLJ60983, Large proline-rich prot. BAT3

A E I G E G A Y G K V FCell division prot. kinase 6

Q E Q E I D G K S L L Lalpha motif domain containing 13 isof. 2

E E M P A T K G G F S FNuclear pore complex prot. Nup153

A E K A T D A T T A T FC14orf118 hypothetical prot. LOC55668 isof. 2

Q E L D S T D G A K V F signal recognition particle 54kDa isof. 2

A E L A K V I N D G L FIsof. 2 of La-related prot. 1

S E M D T G N D D K H T LIsof. 2 of receptor potential channel 4-associate

A E V G V L V G K D R S S FProfilin-1

N E F S I L K S P G S V V F FLJ59925, highly similar to Renin receptor

K E I E L I G S G G F G Q V FEIF2AK2 prot.

Q E S G G F S G P G E N R S MEwing sarcoma breakpoint region 1 isof. 5