2251 KSFFLSH 1 Phage display (subtractive panning) 2 PMID:23714122 Pancreatic metastasis Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) GI-LI-N-derived primary tumor was used in the negative selelction. And corresponding pancreatic metastasis was used in the positive selection. Fifteen phage clones were selected for binding to the metastatic mass. 2252 YEGLISR 1 Phage display (subtractive panning) 3 PMID:23714122 HTLA-230-derived primary tumor Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Pre-selection on HTLA-230 cells was performed. Then selection on HTLA-230-derived primary tumor was carried out. 2253 HSYWLRS 1 Phage display (subtractive panning) 4 PMID:23714122 GI-LI-N-derived primary tumor Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Pre-selection on GI-LI-N cells was performed. Then selection on GI-LI-N-derived primary tumor from a different mouse was carried out. 2254 WSWPREL ALAAHKL 2 Phage display (subtractive panning) 4 PMID:23714122 GI-LI-N-derived primary tumor Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Pre-selection on GI-LI-N cells was performed. Then selection on GI-LI-N-derived primary tumor from a different mouse was carried out. 2255 SNYDTMLMHAKR[2.546 ± 0.154] TWNGTSNYDWPN[1.636 ± 0.118] SSNYHNKLHGEL[1.840 ± 0.131] AMLSPYDTNPWN[1.467 ± 0.067] ATDNYTTRAPRH[1.342 ± 0.101] ANPGQNPYEKRE[1.523 ± 0.120] QWFKSPLDVRHS[1.132 ± 0.096] GIGNFERYYGTA[2.123 ± 0.112] MPRRTRSIIISS[1.059 ± 0.086] SPRLTTYKASPK[1.800 ± 0.079] SNYD 10 Phage display (common panning) 3 PMID:23747319 Anti-NS2 4D4 mAb NS2 Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA The affinities of selected phages to anti-NS2 4D4 mAb were measured by ELISA. Absorbance at 492 nm was determined, reproduced from the graph and expressed as mean ± SD. Phage ELISA results showed that the selected ten phage clones had high reactivity with mAb 4D4 (OD492 nm > 1.0) compared to a negative control of irrelevant mAb, the anti-porcine IFN-γ mAb (OD492 nm < 0.20). After three successive rounds of biopanning, phage ELISA results showed that the selected ten phage clones had high reactivity with mAb 4D4 (OD492 nm > 1.0) compared to a negative control of irrelevant mAb. 2256 CKSLEYSYC(18) CKSPENSYC(6) CTNTLSNNC(5) CTNTLNYNC(2) CKSTENSYC(1) CKSPENYYC(1) CKSPENYNC(1) CKSLENYYC(1) CKSMENSYC(1) CKYTESYNC(1) CKYLENSYC(1) CKSPENSSC(1) CNNTQSYNC(1) CTTPGNYNC(1) CKTRENSYC(1) CKSTQNSNC(1) CKNTENYNC(1) 17 Phage display (subtractive panning) 3 PMID:20709321 Pb2+ Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was first screened against uncharged monolithic column. Three rounds of main biopanning were conducted against Pb2+ as a target. The phage sample from the third round of positive selection was screened against uncharged monolithic column (post-negative screening I). After three rounds, the amplified phages were used in the next post-negative screening (post-negative screening II) against various other metal ions. Three rounds of negative selection against Cu2+, three rounds against Ni2+, two rounds against Co2+ and one round against Fe3+ were conducted. Sixty individual clones were sent for sequencing and 44 DNA sequences were obtained. 2257 TRWLVYFSRPYLVAT(9) 1 Phage display (common panning) 4 PMID:23806589 Anti-blood group A antigen monoclonal antibody Blood group A antigen Not determined. Not determined. f3-15mer phage display library (X15) Thirty-seven phage clones were chosen randomly and amplified. Eleven positive phage clones' exogenous DNAs were sequenced and the corresponding peptides were deduced. Among these eleven phage clones, nine clones displayed the same peptide - TRWLVYFSRPYLVAT, the other two phage clones displayed two different peptides respectively. 2258 NAHLQSDALPQT(7)[2.152 ± 0.045] WHWFRYPAPPPE(2)[2.152 ± 0.045] QVVSDNRWPTMK(1)[2.301 ± 0.033] WHYNWWLPAGPR(1)[2.626 ± 0.045] SISWWRWHWASV(1)[2.142 ± 0.087] HLYHYSYAAYWP(1)[2.274 ± 0.122] FHWSWYTPSRPS(1)[1.987 ± 0.100] 7 Phage display (common panning) 3 PMID:23707345 Anti-TTPI 4H11D10B11 mAb Triosephosphate isomerase, TPI Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Phage clones with mimotopes (1–7) were tested with ELISA to evaluate their reactivity to monoclonal antibody. TTPI was used as positive control and a M13 phage without insert (M13KE) and an unrelated mimotope (TsGST25) were used as negative controls of antigens. Additionally, anti-T. gondii mAb was tested in parallel as negative control (data not shown). Absorbance at 492 nm was determined, reproduced from the graph and expressed as mean ± SD. The absorbances of TTPI, M13KE and TsGST25 were 2.362 ± 0.120, 0.049 and 0.082, respectively. A total of 14 peptides were obtained after three rounds of panning of a random peptide phage display library (12 mer) using the 4H11D10B11 mAb. 2259 HHKTWHPPVMHL(8)[1.415 ± 0.061] SQWHPRSASYPM(2)[1.355 ± 0.035] WHP 2 Phage display (common panning) 4 PMID:23664850 Spike glycoprotein Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Ten selected phages were incubated with the SARS-CoV S1 protein in ELISA plates to determine the specific binding activities for the protein. Three independent experiments were repeated for each individual. The OD492 value of tested individual phage was determined, reproduced from the graph and expressed as mean ± SD. The absorbances of phages with the same sequence were calculated as mean ± SD. The value of the negative control was 0.377 ± 0.071. The binding activities of 10 selected phages were assayed using ELISA. The results revealed that they had a specific binding activity to the SARS-CoV S1 protein. 2260 YGNAPDKPLSKR[1.327] TERAPDSPTSKS[1.443] ALLWEAPDQRLS[1.665] TERPPDSPASKS[1.572] STSPDFPLSSFY[1.603] HSHHTLTPDPPL[1.443] YAPTPPLSRIDP[1.567] ALHHHASRDAPE[1.340] APDPPLSR 8 Phage display (common panning) 3 PMID:23261158 Anti-CsdA A3G5 mAb Cold-shock DEAD-box protein A, CsdA Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA The reactivities of selected phages with the mAb were assessed by indirect ELISA analysis. Absorbance at 450 nm was determined, reproduced from the graph and shown. The absorbances of the negative and positve phages were 0.225 and 1.799, respectively. The results showed that these 10 single phages expressed peptides that interacted with mAb A3G5 (OD450 nm > 0.3). These interactions were specific because no interaction was detected in the BSA control wells (OD450 nm < 0.08). 10 positive phage clones were randomly selected after three rounds of bio-panning and identified by ELISA. Eight of these clones were sequenced, and their amino acid sequences were deduced. 2261 DWLVWYG 1 Phage display (subtractive panning) 4 PMID:23888692 Toll-like receptor 2 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) 2262 CKTVPDNHC CDSPLTRNC CIGKFLYRC 3 Phage display (common panning) 3 PMID:23502767 MD-2 mimic peptide, NH2-FSKGKYKCV-COOH Lipopolysaccharide, LPS Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Western blot The Western blot (WB) analysis showed clearly that AP6 (CKTVPDNHC) and AP11 (CDSPLTRNC) indeed bound the MD-2 molecule. After 3 rounds of selection, 15 plaques were identified and their culture supernatants'ability to inhibit the production of cytokines was tested in PMA-induced U937 cells stimulated with LPS. Of the 15 clones, #5, #6, #8, #10, and #11 demonstrated good inhibition of TNFa and IL-6 production. We selected clones CKTVPDNHC, CDSPLTRNC, and CIGKFLYRC for further investigation as these 3 clones shows more inhibition effects than others. 2263 APTAVCNFFGQCPMEI APSKVCAHFDICYTLP APTTPCRKYFMCWEAG ALPKSCRILGTCQSIN 4 Phage display (common panning) 3 PMID:11179221 G protein β1γ1 subunits Not determined. Not determined. Not determined. f88-4 phage display library pool 2264 CGIHPWTKC(12/28) CGRWGHIPC(5/28) 2 Phage display (subtractive panning) 6 PMID:17125317 Single-walled carbon nanotubes, SWNTs Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was preincubated with a graphite suspension to minimize the isolation of graphite-selective phage. Panning experiments were performed by mixing the recovered phages with the SWNT suspension. Biopanning was repeated six times with increasing Tween-20 concentrations (i.e., 0.2, 0.3, 0.4, 0.5, 0.75, and 1.0%). A new motif, X1THX2X3PWTX4, where X1 is G or H, X2 is H or D or null, X3 is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. 2265 CHTHNPWTC(3/15) 1 Phage display (subtractive panning) 5 PMID:17125317 Single-walled carbon nanotubes, SWNTs Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was preincubated with a graphite suspension to minimize the isolation of graphite-selective phage. Panning experiments were performed by mixing the recovered phages with the SWNT suspension. Biopanning was repeated six times with increasing Tween-20 concentrations (i.e., 0.2, 0.3, 0.4, 0.5 and 0.75%). A new motif, X1THX2X3PWTX4, where X1 is G or H, X2 is H or D or null, X3 is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. 2266 CHTHPWTKC(3/11) 1 Phage display (subtractive panning) 4 PMID:17125317 Single-walled carbon nanotubes, SWNTs Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The phage library was preincubated with a graphite suspension to minimize the isolation of graphite-selective phage. Panning experiments were performed by mixing the recovered phages with the SWNT suspension. Biopanning was repeated four times with increasing Tween-20 concentrations (i.e., 0.2, 0.3, 0.4 and 0.5%). A new motif, X1THX2X3PWTX4, where X1 is G or H, X2 is H or D or null, X3 is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. 2267 ATNAPRYTMQWS(5/15) EHMALTYPFRPP(3/15) 2 Phage display (subtractive panning) 5 PMID:17125317 Single-walled carbon nanotubes, SWNTs Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The phage library was preincubated with a graphite suspension to minimize the isolation of graphite-selective phage. Panning experiments were performed by mixing the recovered phages with the SWNT suspension. Biopanning was repeated six times with increasing Tween-20 concentrations (i.e., 0.2, 0.3, 0.4, 0.5 and 0.75%). A new motif, X1THX2X3PWTX4, where X1 is G or H, X2 is H or D or null, X3 is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. 2268 LLADTTHHRPWT(3/10) 1 Phage display (subtractive panning) 4 PMID:17125317 Single-walled carbon nanotubes, SWNTs Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The phage library was preincubated with a graphite suspension to minimize the isolation of graphite-selective phage. Panning experiments were performed by mixing the recovered phages with the SWNT suspension. Biopanning was repeated four times with increasing Tween-20 concentrations (i.e., 0.2, 0.3, 0.4 and 0.5%). A new motif, X1THX2X3PWTX4, where X1 is G or H, X2 is H or D or null, X3 is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. 2269 LPIFKVDFGDHSPFT(1) ARMFLLFLMRCIGCY(1) SHSFSVGSGDHSPFT(2) SHSFSVGSGDHSPFT(2) SHSFSVGSGSGDHSP(1) LSFFSCWLRRSFSLT(1) EVPRLSLLAVFLVVM(1) EVPRLSLLAVFLCNG(1) EVPRLSLLAVFLVAN(2) GRFLTGGTGRLLRIS(1) 10 Phage display (subtractive panning, in vivo) 3 PMID:23935860 Glutamate carboxypeptidase 2 EC=3.4.17.21 Not determined. Not determined. Not determined. f3-15mer phage display library (X15) Poly-histidine tagged PSMA (PSMA-His6) is actually the target. A 15-mer library was screened against the soluble ectodomain of PSMA. In the initial step, the library was pre-cleared by intravenous administration in a mouse to remove phages that bound to vascular proteins thus clearing the phage pool of non-specific binders. After the third round of selection, three strong consensus sequences emerged: GDHSPFT, SHFSVGS and EVPRLSLLAVFL, where the former sequence appeared three times and the latter two sequences appeared four times. 2270 IDPVGWGNERTFQVP(8/8) 1 Phage display (common panning) 4 PMID:10975844 Monoclonal antibody TP25.99 β2m-free or β2m-associated HLA class I heavy chains Not determined. Not determined. f3-15mer phage display library (X15) Microwells were coated with avidin. The first round of panning was performed using 1.0e12 phage particles in TBS 50 and 1mg biotinylated mAb TP25.99 per well. The subsequent three rounds of selection were conducted using 1.0e10 phage particles and 0.1μg biotinylated mAb per well. We have mapped the conformational and the linear determinants recognized by mAb TP25.99 on HLA class I heavy chains. This information contributes to our understanding of the structural relatedness of distinct antigenic determinants defined by a mAb and of the conformational changes in HLA class I heavy chains induced by their association with β2m. 2271 QCTNFISDHECH(4/7) SCDGFYTGPACM(2/7) QCVETWNRIECK(1/7) 3 Phage display (common panning) 4 PMID:10975844 Monoclonal antibody TP25.99 β2m-free or β2m-associated HLA class I heavy chains Not determined. Not determined. LX-8 phage display library (XCX8CX) Microwells were coated with avidin. The first round of panning was performed using 1.0e12 phage particles in TBS 50 and 1mg biotinylated mAb TP25.99 per well. The subsequent three rounds of selection were conducted using 1.0e10 phage particles and 0.1μg biotinylated mAb per well. We have mapped the conformational and the linear determinants recognized by mAb TP25.99 on HLA class I heavy chains. This information contributes to our understanding of the structural relatedness of distinct antigenic determinants defined by a mAb and of the conformational changes in HLA class I heavy chains induced by their association with β2m. 2272 CWASNPSLC(1) CPYSNPSLC(1) CPFANPSTC(1) CNFSNPSLC(3) CEHSNPSLC(1) CWAANPSMC(1) CPFSNPSMC(1) CPYANPSLC(1) CSWANPSQC(1) CMFSNPSLC(1) CPFANPSMC(1) NPS 11 Phage display (subtractive panning) 3 PMID:16223774 Anti-CD20 monoclonal antibody rituximab B-lymphocyte antigen CD20 Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) At each round, phage particles binding to isotypic and allotypic determinants of rituximab were removed by a preadsorption step on the rituximab isotype-matched infliximab. The epitope(s) recognized by Rp15-C (CPYANPSLC) is within the rituximab Ag-combining site. 2273 WPRWLEN(9) 1 Phage display (subtractive panning) 3 PMID:16223774 Anti-CD20 monoclonal antibody rituximab B-lymphocyte antigen CD20 Not determined. Not determined. Ph.D.-7 phage display library (X7) At each round, phage particles binding to isotypic and allotypic determinants of rituximab were removed by a preadsorption step on the rituximab isotype-matched infliximab. The epitope(s) recognized by Rp1-L (WPRWLEN) is within the rituximab Ag-combining site. 2274 EGHEHQTSWWEL(1) QDKLTQWPKWLE(5) HTSVERWPLWLE(1) ITPWPHWLERSS(1) TTTTSVWPAWLE(2) W-P-x-W-L-E 5 Phage display (subtractive panning) 3 PMID:16223774 Anti-CD20 monoclonal antibody rituximab B-lymphocyte antigen CD20 Not determined. Not determined. Ph.D.-12 phage display library (X12) At each round, phage particles binding to isotypic and allotypic determinants of rituximab were removed by a preadsorption step on the rituximab isotype-matched infliximab. The epitope(s) recognized by Rp5-L (QDKLTQWPKWLE) is within the rituximab Ag-combining site. 2275 TSPFTPVIGPLEHRS(1) STTNTPLVSHLEHRS(1) TGSVYSPTGLLEHRS(1) RETKLPFNVYTEHRS(1) XPPFTSAVGGVDHRS(1) APPFTSAVGGVDHRS(1) MDDDTERFPTHRSLP(1) RARDHSSTAQQEHAT(1) RAMAGRCRLLLSIGS(1) LEHRSPAE 9 Phage display (common panning) 3 PMID:10423148 Anti-gG2 monoclonal antibody H5 Envelope glycoprotein G, gG, gG-2 Not determined. Not determined. f88-15mer phage display library (X15) After three rounds of biopanning, individual phage clones were isolated and screened by ELISA to identify those which bound strongly to the antibody of interest, and those which gave a clear positive signal were sequenced.