Methods and compositions for assessing antibody specificities

Abstract

The present invention provides compositions and methods that can be used to determine a peptide signature for an antibody repertoire in a sample comprising multiple antibodies. The of an antibody specificity in method can be used to characterize a phenotype in a sample, such as providing a diagnosis, prognosis or theranosis of a medical condition.

1 . A method of characterizing a phenotype in a biological sample comprising:
 a) identifying at least one peptide motif in the biological sample comprising:
 i) providing a biological sample comprising a plurality of antibodies; 
 ii) contacting the biological sample with a plurality of peptides; and 
 iii) identifying members of the plurality of peptides that form a complex with members of the plurality of antibodies; 
 iv) determining at least one peptide motif from the members of the plurality of peptides identified in iii), wherein determining the at least one peptide motif comprisesaligning the sequences of the members of the plurality of peptides identified in iii); and wherein the aligning comprises using a computational alignment algorithm; 
   b) comparing the presence or level of the at least one peptide motif identified in step a) to a reference value; and   c) identifying at least one peptide motif with a presence or level that differs from the reference based on the comparison in b),   thereby identifying the at least one peptide motif indicative of the phenotype.   
     
     
         2 . The method of  claim 1 , wherein the biological sample is any one or more of peripheral blood, lymphatic fluid, cerebral spinal fluid, sweat, urine, saliva, mucus, or a derivative of any thereof. 
     
     
         3 . The method of  claim 1 , wherein the reference value comprises a presence or level of the same peptide motif in a control sample. 
     
     
         4 . The method of  claim 3 , wherein the control sample has a different phenotype than the biological sample. 
     
     
         5 . The method of  claim 1 , wherein the phenotype comprises a disease or disorder. 
     
     
         6 . The method of  claim 1 , wherein the characterizing comprises diagnosis, prognosis or theranosis of the disease or disorder. 
     
     
         7 . The method of  claim 5 , wherein the disease is an infectious disease or an autoimmune disease. 
     
     
         8 . The method of  claim 7 , wherein the infectious disease is a bacterial infection, a viral infection or a parasitic infection. 
     
     
         9 . The method of  claim 8 , wherein the bacterial infection is a  Streptococcus  sp. infection,  Borrelia  infection,  Ehrlichia  infection,  Anaplasma  infection, or  Babesia  infection. 
     
     
         10 . The method of  claim 9 , wherein the presence of the at least one peptide motif selected from [IV]X[PR]QPEKP (SEQ ID NO: 66), KXDDMLN (SEQ ID NO: 67), KXDXMLN (SEQ ID NO: 68), LW]XSAEXEEK (SEQ ID NO: 69), SAEXEXK (SEQ ID NO: 70) or combinations thereof, wherein X is any amino acid, is indicative of a  Streptococcus  sp. infection. 
     
     
         11 . The method of  claim 9 , wherein the presence of the at least one peptide motif selected from VQQExxxxxP (SEQ ID NO: 358), QQEGxxxx[YC] (SEQ ID NO: 359), QEG[IV]Q (SEQ ID NO: 360), G[IV]QxEG (SEQ ID NO: 361), [LI]xxA[ILV]xxRG (SEQ ID NO: 362), [ATNSD]xxxxAl[LAM]xR (SEQ ID NO: 363), Ix[LM]xGFxK (SEQ ID NO: 364), LxGM[RQ]K (SEQ ID NO: 365), [HR]xDxTNxF (SEQ ID NO: 366), [DA]DPTN (SEQ ID NO: 367), [KR]x[DE]xTNxF (SEQ ID NO: 368), [ET][ML]HKF (SEQ ID NO: 369), [ML]xxEFHK (SEQ ID NO: 370), Q[TI]EQxxxxxK (SEQ ID NO: 371), DxSP[IL]E (SEQ ID NO: 372), PFx[AP]YxK (SEQ ID NO: 373), VxxYFxx[LV]xK (SEQ ID NO: 374), KxVDxDR (SEQ ID NO: 375), [DN][AS]A[AG]F (SEQ ID NO: 376), Cx[NA]xKFC (SEQ ID NO: 377), Kx[GRST]AE[YF] (SEQ ID NO: 378), HQV[PA]xxx[DHE] (SEQ ID NO: 379), IPxxV[IF]xxR (SEQ ID NO: 380), Cx[ALT]xWEx[CA] (SEQ ID NO: 381), CxxxCA[IL]xxR (SEQ ID NO: 382), I[IV]Ixx[MT]xK (SEQ ID NO: 383), QG[ITL]x[KN][FY] (SEQ ID NO: 384), KxxPPxIN (SEQ ID NO: 385), G[YF][FY]FxxK (SEQ ID NO: 386), DKNVx[IV] (SEQ ID NO: 387), [QE][KR][ND]xSG (SEQ ID NO: 388), K[RK]PGD (SEQ ID NO: 389), EGAxQP (SEQ ID NO: 390), GSPEY (SEQ ID NO: 391) or combinations thereof, wherein X is any amino acid, is indicative of  Borrellia burdorferi  infection. 
     
     
         12 . The method of  claim 9 , wherein the presence of the at least one peptide motif selected from YxxL[IV]xP[KR] (SEQ ID NO: 586), [SA]Nx[ML]FY (SEQ ID NO: 587), WDGSx[IV] (SEQ ID NO: 588), PxxL[IV]KP (SEQ ID NO: 589), KxDWDG (SEQ ID NO: 590), RxxxxKxD[HY]D (SEQ ID NO: 591), VDVMGN (SEQ ID NO: 592), Ex[NQ][QN]xFY (SEQ ID NO: 593), Vx[TS][TS]N (SEQ ID NO: 594), KLHDP (SEQ ID NO: 595), KxDxDT[GN] (SEQ ID NO: 596), Y[HA]GWx[ SAE] (SEQ ID NO: 597), NPEH[DTE] (SEQ ID NO: 598), NPAxQ[HR] (SEQ ID NO: 599), [KR]MNKxx[TP] (SEQ ID NO: 600), DWxxx[FY][VK]K (SEQ ID NO: 601), GVN[APTS]xK (SEQ ID NO: 602), [IV]x[PR]EGxK (SEQ ID NO: 603), RVF[ST][MA] (SEQ ID NO: 604), NxRxx[VI]W[YF] (SEQ ID NO: 605), Yxx[MTL]xYNA (SEQ ID NO: 606), Kx[VI]x[ND][IV]W (SEQ ID NO: 607), [ED][YF]Q[LQ]H (SEQ ID NO: 608), FGxPSI (SEQ ID NO: 609), QLVGxxK (SEQ ID NO: 610), YxxL[IV]xP[KR] (SEQ ID NO: 611) or combinations thereof, wherein X is any amino acid, is indicative of  Erlichia  sp. Infection. 
     
     
         13 . The method of  claim 9 , wherein the presence of the at least one peptide motif selected from W[YK]Wx[PA]K (SEQ ID NO: 612), KxExH[NK]F (SEQ ID NO: 613), QxxxWPYxK (SEQ ID NO: 614), YxFDxNxR (SEQ ID NO: 615), FxWN[VI]P (SEQ ID NO: 616), [FW][LM]EXAH (SEQ ID NO: 617), DF[LI]xAT (SEQ ID NO: 618), KxMSxFV (SEQ ID NO: 619), W[YK]Wx[PA]K (SEQ ID NO: 620), KxExH[NK]F (SEQ ID NO: 621), QxxxWPYxK (SEQ ID NO: 622), WPT[SF]T (SEQ ID NO: 623), WP[TA]GR (SEQ ID NO: 624), KNWPx[GF] (SEQ ID NO: 625), KxxP[LI]FA (SEQ ID NO: 626), WPxGQV (SEQ ID NO: 627), [VI][LR]KDF (SEQ ID NO: 628), WPT[SF]T (SEQ ID NO: 629), Kx[IM][VN]xWA (SEQ ID NO: 630), [YW]TxEPF (SEQ ID NO: 631), [AM][PTS]WExF (SEQ ID NO: 632), R[PT][RTK]F[NS] (SEQ ID NO: 633), VY[SA]HW (SEQ ID NO: 634), [WF]xxKPxWxxM (SEQ ID NO: 635), KGx[SA]HxF (SEQ ID NO: 636), KGxVxF[AS] (SEQ ID NO: 637), [IV]xHxTID (SEQ ID NO: 638), MLSXXVN (SEQ ID NO: 639), KxYSxxVR (SEQ ID NO: 640), Kx[VK]VNP (SEQ ID NO: 641) or combinations thereof, wherein X is any amino acid, is indicative of  Anaplasma  sp. infection. 
     
     
         14 . The method of  claim 8 , wherein the viral infection is an HIV infection, Hepatitis infection, HSV-1 infection, Zika virus infection, Rhinovirus infection, Cytomegalovirus infection, or Epstein Barr virus infection. 
     
     
         15 . The method of  claim 14 , wherein the presence of the at least one peptide motif selected from LFGxx[LM]N (SEQ ID NO: 9), GELxGQ (SEQ ID NO: 852), EWVxx[YF]D (SEQ ID NO: 10), P[LM]ALxL(SEQ ID NO: 11), KxNExWxV (SEQ ID NO: 12), P[AG]xRTxK (SEQ ID NO: 13), AYTxVN (SEQ ID NO: 14), WN[AS]YxxxN (SEQ ID NO: 15), [RKE]xxWxP[LM]Q (SEQ ID NO: 16), [AS]YxSx[SA][YF] (SEQ ID NO: 17), ExYxSPS (SEQ ID NO: 18), MNIxDD (SEQ ID NO: 19), EH[ANK]FW (SEQ ID NO: 20), VHNAY (SEQ ID NO: 21), HG[EA]xLN (SEQ ID NO: 22), [GD]xx[LF]xxP[ML]Q (SEQ ID NO: 23), [LVIVII]xNAx[TS][FGI] (SEQ ID NO: 24), PxNSYT (SEQ ID NO: 25), RxxPLAxxL (SEQ ID NO: 26), CPKxNxT (SEQ ID NO: 27), Q[PA]H[AM]F (SEQ ID NO: 28), PAxENxxx[GSP] (SEQ ID NO: 29), NID[DE]D (SEQ ID NO: 30); RxQx[VS]D[NA] (SEQ ID NO: 31), Wx[DP]PxHL (SEQ ID NO: 32), TWA[FI][FI] (SEQ ID NO: 33), EDxGHP (SEQ ID NO: 34); [ETA]xxx[YF]xxP[SR]Q (SEQ ID NO: 35); GMxP[RK]Q (SEQ ID NO: 36), Wxx[VI]RxxPxQ (SEQ ID NO: 37), [NE][AG]Y[SAT]xxW (SEQ ID NO: 38), KxI[ST]xYW (SEQ ID NO: 39), YYxYRxxK (SEQ ID NO: 40), KxHExG[FY (SEQ ID NO: 41)], [MLF]xNPQQ, HHFL[VI] (SEQ ID NO: 42), [LV]CNAY (SEQ ID NO: 43) or combinations thereof, wherein X is any amino acid, is indicative of mononucleosis by EBV infection. 
     
     
         16 . The method of  claim 14 , wherein the presence of the at least one peptide motif selected from L[EDQ]EV[LIV][IV][DE]K (SEQ ID NO: 50), E[VI][VIL][IV][DEN]K (SEQ ID NO: 51), E[VI][VI][VI]XK (SEQ ID NO: 52), VXPNI (SEQ ID NO: 53), VVPN (SEQ ID NO: 54), LXEVLVVVP (SEQ ID NO: 55), GPXHTXKV (SEQ ID NO: 56), EXY[VI]DX[VT]LN (SEQ ID NO: 57) or combinations thereof, wherein X is any amino acid, is indicative of a Rhinovirus infection. 
     
     
         17 . The method of  claim 14 , wherein the presence of the at least one peptide motif selected from KXDPDXXW[ST] (SEQ ID NO: 62), KPXLGGK (SEQ ID NO: 63) or combinations thereof, wherein X is any amino acid, is indicative of a Cytomegalovirus infection. 
     
     
         18 . The method of  claim 14 , wherein the presence of at least one peptide motif selected from GRRPFF (SEQ ID NO: 269), GGGxGAGGG (SEQ ID NO: 270), EG[PA]ST[GA]R (SEQ ID NO: 271), KXXSC[IVL]GC[RK] (SEQ ID NO: 272), SCIGCK (SEQ ID NO: 273), CIGC (SEQ ID NO: 274), VxLPHW (SEQ ID NO: 275), LPHW (SEQ ID NO: 276), PQDT[GA]PR (SEQ ID NO: 277), GPPWWP (SEQ ID NO: 278), QQPTTXGW (SEQ ID NO: 279), [LMIV]FDXDWYP (SEQ ID NO: 280) or combinations thereof, wherein X is any amino acid, is indicative of an Epstein-Barr virus (EBV) infection. 
     
     
         19 . The method of  claim 14 , wherein the presence of at least one peptide motif selected from CxGxLIC(SEQ ID NO: 290), CxxKx[IV]C[IV] (SEQ ID NO: 291), W[GAS]CxGxxxC (SEQ ID NO: 292), [RK]KL[IV]E (SEQ ID NO: 293), KLIMT (SEQ ID NO: 294), [QE]xxPFRY (SEQ ID NO: 295), CxxKx[IV]C[IV] (SEQ ID NO: 296), [LF]xx[LIV][ND]KW (SEQ ID NO: 297), [AP][GC]GFG (SEQ ID NO: 298), LIx[TS]TY (SEQ ID NO: 299), [RK]KLxx[MV]Y (SEQ ID NO: 300), GF[GA][AQ][AYV] (SEQ ID NO: 301), GFG[RQ]x[FNY] (SEQ ID NO: 302), [KR]KxIH[VIM] (SEQ ID NO: 303), R[IV]PFG (SEQ ID NO: 304), KLIxx[TY]T (SEQ ID NO: 305) or combinations thereof, wherein X is any amino acid, is indicative of an HIV infection. 
     
     
         20 . The method of  claim 14 , wherein the presence of at least one IgG peptide motif selected from VRxxYxQH (SEQ ID NO: 319); CEDxxxHxC (SEQ ID NO: 320); DAEQxxR (SEQ ID NO: 321); WPGIF (SEQ ID NO: 322); CCYDXE (SEQ ID NO: 323); LxPDNxT (SEQ ID NO: 324); FxWGQxY (SEQ ID NO: 325); KxEGHxxxxA (SEQ ID NO: 326); CxxGxCQxK (SEQ ID NO: 327); CCxDxx[DE][ED] (SEQ ID NO: 328); RNGxED (SEQ ID NO: 329); [DE]xRxIYxQ (SEQ ID NO: 330); WxRCGL (SEQ ID NO: 331); D[ED]xRxxYxxH (SEQ ID NO: 332); WCxLx[AV]N (SEQ ID NO: 333); LXTPWI (SEQ ID NO: 334); CWxxxGL[CA] (SEQ ID NO: 335); ID[AV]EP (SEQ ID NO: 336); HF[NK][VT]xK (SEQ ID NO: 337); QxNHQxK (SEQ ID NO: 338) or combinations thereof, wherein X is any amino acid, is indicative of a Zika virus infection. 
     
     
         21 . The method of  claim 14 , wherein the presence of at least one IgM peptide motif selected from FExKEP (SEQ ID NO: 339), [FYW]DA[VI] (SEQ ID NO: 340), DFDKR (SEQ ID NO: 341), WETC (SEQ ID NO: 342), KLDGP (SEQ ID NO: 343), WIYPxK (SEQ ID NO: 344), V[HS]DSK (SEQ ID NO: 345), EQCGT (SEQ ID NO: 346), [KE][MVIT]PYA (SEQ ID NO: 347), [DE]xxML[RP]W (SEQ ID NO: 348), YExLHx[FY] (SEQ ID NO: 349), WY[TSN]xEK (SEQ ID NO: 350), [YF]H[DNS]AV (SEQ ID NO: 351), DxTG[VI]P (SEQ ID NO: 352), FDxxGEH (SEQ ID NO: 353), QC[AK]xx[HE]C (SEQ ID NO: 354), LW[FY]xPxE (SEQ ID NO: 355), C[MI][PA]GxxC (SEQ ID NO: 356), Cxxxx[AVS]ADC(SEQ ID NO: 357), TTESxV (SEQ ID NO: 854), KDV[GA]E(SEQ ID NO: 855), KPxD[FWM]GxK(SEQ ID NO: 856), VxADGT(SEQ ID NO: 857), M[AP][AT]AD (SEQ ID NO: 858), VPxPK[DG](SEQ ID NO: 859), QxKP[TS]D(SEQ ID NO: 860), F[TS]xDGF(SEQ ID NO: 861), Wx[RK]VY[VA](SEQ ID NO: 862), [CS]T[TS]Exxx[YF](SEQ ID NO: 863), YxETC[TI](SEQ ID NO: 864) or combinations thereof, wherein X is any amino acid, is indicative of a Zika virus infection. 
     
     
         22 . The method of  claim 14 , wherein the presence of MKEAX[SA]EK (SEQ ID NO: 497) is indicative of  Haemophilus influenza  infection. 
     
     
         23 . The method of  claim 8 , wherein the parasitic infection is a  Trypanosoma cruzi  infection,  Toxoplasma gondii  infection,  Taenia solium  infection or  Toxocara canis  infection. 
     
     
         24 . The method of  claim 23 , wherein the presence of the at least one peptide motif selected from [RK]MRxID (SEQ ID NO: 104); QHxGHP (SEQ ID NO:
 105); KxxLPED (SEQ ID NO: 106); [IV]LxxFGY (SEQ ID NO: 107); PLDxxxxIS (SEQ ID NO: 108); ETXIPXE (SEQ ID NO: 109); [VI]Nx[DE][ML]YxP (SEQ ID NO: 110); FLxxIGA (SEQ ID NO: 111); D[VI]x[MI][ILV]x[KR] (SEQ ID NO: 112); RxSPYx[IL]F (SEQ ID NO: 113); VGPRH (SEQ ID NO: 114); PQxQH[ED] (SEQ ID NO: 115); PxxGGFG (SEQ ID NO: 116); KxEGxxMG (SEQ ID NO: 117); KxxGxTxxLS (SEQ ID NO: 118); EMG[FW]Q (SEQ ID NO: 119); [VI]KxGxxDxP (SEQ ID NO: 120); PE[DN]ExYP (SEQ ID NO: 121); HYEWA (SEQ ID NO: 122); [HR]SNMxF (SEQ ID NO: 123); M[TV]GxxYE (SEQ ID NO: 124); Dxx[KH]ExxLL (SEQ ID NO: 125); RxxWx[EDA]x[IV][AR] (SEQ ID NO: 126); PxDxxAx[GPA][TS] (SEQ ID NO: 127); PDxxSxT[ARG] (SEQ ID NO: 128); GRExDG (SEQ ID NO: 129); GVPGxxxK (SEQ ID NO: 130); [LM]xxx[EDQ]VxxIM (SEQ ID NO: 131); SxxxVSGG (SEQ ID NO: 132); A[KR]AG[DN]K (SEQ ID NO: 133); F[RN]xIN[RQ] (SEQ ID NO: 134); YXPVXPXSY (SEQ ID NO: 135); KxTFPD (SEQ ID NO: 136); PFM[FVM]xxR (SEQ ID NO: 137); EFWEP (SEQ ID NO: 138); [FY]GALS (SEQ ID NO: 139); PxGTEN (SEQ ID NO: 140); Gx[KE]PWE (SEQ ID NO: 141); D[IV]Tx[YF][WN] (SEQ ID NO: 142) or combinations thereof, wherein X is any amino acid, is indicative of  Trypansoma cruzi  infection.   
     
     
         25 . The method of  claim 23 , wherein the presence of at least one peptide motif selected from HExE[FY]Q (SEQ ID NO: 74); LD[MLF]WxE (SEQ ID NO: 75) ; HCSAC (SEQ ID NO: 76) ; [FY]xGVVN (SEQ ID NO: 77); KxxxGRGxI (SEQ ID NO: 78); GPH[LA]E (SEQ ID NO: 79); PRREP (SEQ ID NO: 80); CNxxxECY (SEQ ID NO: 81); KxCQPxxC (SEQ ID NO: 82); PxPD[FH][TS] (SEQ ID NO: 83); NxxxExY[AG]xD (SEQ ID NO: 84); P[AG]AxxLD (SEQ ID NO: 85); MPSxSxE (SEQ ID NO: 86); [RK]xYxHR[TS] (SEQ ID NO: 87); K[PA]xFxFxK (SEQ ID NO: 88); DD[CST]xGxR (SEQ ID NO: 89); P[ML]xxHxMY (SEQ ID NO: 90); Kx[ASQ][SAT]xRG (SEQ ID NO: 91); [DG]QPEN (SEQ ID NO: 92); [KHR]N[QN]DG (SEQ ID NO: 93); Nx[EVS]GExY (SEQ ID NO: 94); EP[VI]TG (SEQ ID NO: 95); HGM[PA][KR] (SEQ ID NO: 96); [VIT]PWIF (SEQ ID NO: 97); Kx[STN]VxFQ (SEQ ID NO: 98); [VAI]WSGS (SEQ ID NO: 99); FS[LIAM]xxWG (SEQ ID NO: 100); PTN[PQ]G (SEQ ID NO: 101); [RK]Kxx[YW]xHx[TS] (SEQ ID NO: 102); [HRW]xxHPRF (SEQ ID NO: 103) or combinations thereof, wherein X is any amino acid, is indicative of Toxoplasma gondii infection. 
     
     
         26 . The method of claim  23 c1aim 22, wherein the presence of at least one peptide motif selected from AxSPN[QEA] (SEQ ID NO: 226); [RP]xAxSxNx[IFMLV] (SEQ ID NO: 227); PDxGVxP (SEQ ID NO: 869); NxxLGL[VT] (SEQ ID NO: 228); [YF]x[DE]IxxFF (SEQ ID NO: 229); IxHFFxG (SEQ ID NO: 230); [ILM][ILM][RK]H[ED]XQ (SEQ ID NO: 231); [ILM][RK]HExQ (SEQ ID NO: 232); KPxx[IL]xLx[KR] (SEQ ID NO: 233); NxDxxYYxx[WF] (SEQ ID NO: 234); GLDGP (SEQ ID NO: 235); RSxHDxxN (SEQ ID NO: 236); FDxFN[IL] (SEQ ID NO: 237); TIFxGK (SEQ ID NO: 238); R[AV]xS[TQ]H (SEQ ID NO: 239); KWHGxY (SEQ ID NO: 240); MPEDK (SEQ ID NO: 241); Exxx[FY]x[AS]D[NT] (SEQ ID NO: 242); NQSxxKx[VI] (SEQ ID NO: 243); KxY[NAS]PY (SEQ ID NO: 244); [PQ][VUHPR] (SEQ ID NO: 245); EDGMxxW (SEQ ID NO: 246); YASXQE (SEQ ID NO: 247); KQxQ[QK]E (SEQ ID NO: 248); K[AS]VFD[IVM] (SEQ ID NO: 249); PN[QE]x[DN]P (SEQ ID NO: 250); P[QA]XM[DN]I (SEQ ID NO: 251); [WR]x[RKH][ST]xFD (SEQ ID NO: 252); KxEPGxK (SEQ ID NO: 253); DDCLP (SEQ ID NO: 254); NXXXXGXHLE (SEQ ID NO: 255); DxxHLEG (SEQ ID NO: 256); RPxx[TS]HN (SEQ ID NO: 257); KxHS[IV]Y (SEQ ID NO: 258); KxHSx[IV]S (SEQ ID NO: 259); MSGYE (SEQ ID NO: 260); YXIWGP (SEQ ID NO: 261); RxxWxMN[RK] (SEQ ID NO: 262); QPxxT[FY]E (SEQ ID NO: 263); YGYNQ (SEQ ID NO: 264) or combinations thereof, wherein X is any amino acid, is indicative of Taenia solium infection. 
     
     
         27 . The method of  claim 7 , wherein the autoimmune disease is Celiac disease. 
     
     
         28 . The method of  claim 27 , wherein the presence of at least one peptide motif selected from QXXXPF[PS]E (SEQ ID NO: 6), PFSEM (SEQ ID NO: 7), PFSEX[FW] (SEQ ID NO: 8), QPXXPFX[ED] (SEQ ID NO: 4) or combinations thereof, wherein X is any amino acid, is indicative of Celiac disease. 
     
     
         29 . A peptide comprising a sequence in any of Tables 1-18. 
     
     
         30 . A composition comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 10000, or at least 100000 peptides matching a peptide sequence in Table 
     
     
         18 . 
     
     
         31 . A composition comprising a library of nucleic acids having sequences encoding at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 10000, or at least 100000 peptides matching a peptide sequence motif in Table 18. 
     
     
         32 . A composition comprising host cells comprising a library of nucleic acids having sequences encoding at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 10000, or at least 100000 peptides matching a peptide sequence motif in Table 18. 
     
     
         33 . (canceled) 
     
     
         34 . (canceled) 
     
     
         35 . A method of depleting a biological sample of an antibody repertoire, comprising:
 a) contacting the biological sample with a composition of  claim 32 ;   b) separating the host cells from the biological sample, thereby depleting the biological sample of the antibody repertoire.   
     
     
         36 . (canceled)