-
1
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold, R. and Mann, M. (2003) Mass spectrometry-based proteomics. Nature, 422, 198–207.
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
2
-
-
2942560894
-
Mass spectrometry as an emerging tool for systems biology
-
Yates, J. R. (2004) Mass spectrometry as an emerging tool for systems biology. Biotechniques, 36, 917–919.
-
(2004)
Biotechniques
, vol.36
, pp. 917-919
-
-
Yates, J.R.1
-
3
-
-
0014007130
-
Determination of the amino acid sequence in oligopeptides by computer interpretation of their high-resolution mass spectra
-
Biemann, K., Cone, C., Webster, B., and Arsenault, G. (1966) Determination of the amino acid sequence in oligopeptides by computer interpretation of their high-resolution mass spectra. J Am Chem Soc, 88, 5598–5606.
-
(1966)
J am Chem Soc
, vol.88
, pp. 5598-5606
-
-
Biemann, K.1
Cone, C.2
Webster, B.3
Arsenault, G.4
-
4
-
-
0027198862
-
Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases
-
Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., and Watanabe, C. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA, 90, 5011–5015.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 5011-5015
-
-
Henzel, W.J.1
Billeci, T.M.2
Stults, J.T.3
Wong, S.C.4
Grimley, C.5
Watanabe, C.6
-
5
-
-
0029645432
-
Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
-
Yates, J., Eng, J., and McCormack, A. (1995) Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem, 67, 3202–3210.
-
(1995)
Anal Chem
, vol.67
, pp. 3202-3210
-
-
Yates, J.1
Eng, J.2
McCormack, A.3
-
6
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
Keller, A., Nesvizhskii, A., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem, 74, 5383–5392.
-
(2002)
Anal Chem
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.2
Kolker, E.3
Aebersold, R.4
-
8
-
-
27944456862
-
Novohmm: A hidden Markov model for de novo peptide sequencing
-
Fischer, B., Roth, V., Roos, F., Grossmann, J., Baginsky, S., Widmayer, P., Gruissem, W., and Buhmann, J. M. (2005) Novohmm: a hidden Markov model for de novo peptide sequencing. Anal Chem, 77, 7265–7273.
-
(2005)
Anal Chem
, vol.77
, pp. 7265-7273
-
-
Fischer, B.1
Roth, V.2
Roos, F.3
Grossmann, J.4
Baginsky, S.5
Widmayer, P.6
Gruissem, W.7
Buhmann, J.M.8
-
9
-
-
18444391517
-
Shotgun identification of protein modifications from protein complexes and lens tissue
-
MacCoss, M., et al. (2002) Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci USA, 99, 7900–7905.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 7900-7905
-
-
Maccoss, M.1
-
10
-
-
0038810081
-
Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry
-
Englander, J., Del Mar, C., Li, W., Englander, S., Kim, J., Stranz, D., Hamuro, Y., and Woods, V. (2003) Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry. Proc Natl Acad Sci USA, 100, 7057–7062.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 7057-7062
-
-
Englander, J.1
Del Mar, C.2
Li, W.3
Englander, S.4
Kim, J.5
Stranz, D.6
Hamuro, Y.7
Woods, V.8
-
11
-
-
34249826390
-
Protein identification via spectral networks analysis
-
Bandeira, N., Tsur, D., Frank, A., and Pevzner, P. (2007) Protein identification via spectral networks analysis. Proc Natl Acad Sci USA, 104, 6140–6145.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 6140-6145
-
-
Bandeira, N.1
Tsur, D.2
Frank, A.3
Pevzner, P.4
-
13
-
-
0037953090
-
Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility
-
Tabb, D., MacCoss, M., Wu, C., Anderson, S., and Yates, JR. (2003) Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal Chem, 75, 2470–2477.
-
(2003)
Anal Chem
, vol.75
, pp. 2470-2477
-
-
Tabb, D.1
Maccoss, M.2
Wu, C.3
Anderson, S.4
Yates, J.R.5
-
14
-
-
1842580753
-
Improving large-scale proteomics by clustering of mass spectrometry data
-
Beer, I., Barnea, E., Ziv, T., and Admon, A. (2004) Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics, 4, 950–960.
-
(2004)
Proteomics
, vol.4
, pp. 950-960
-
-
Beer, I.1
Barnea, E.2
Ziv, T.3
Admon, A.4
-
15
-
-
10644292740
-
Shotgun protein sequencing by tandem mass spectra assembly
-
Bandeira, N., Tang, H., Bafna, V., and Pevzner, P. (2004) Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem, 76, 7221–7233.
-
(2004)
Anal Chem
, vol.76
, pp. 7221-7233
-
-
Bandeira, N.1
Tang, H.2
Bafna, V.3
Pevzner, P.4
-
16
-
-
33644856320
-
Effects of modified digestion schemes on the identification of proteins from complex mixtures
-
Klammer, A. A. and MacCoss, M. J. (2006) Effects of modified digestion schemes on the identification of proteins from complex mixtures. J Proteome Res, 5, 695–700.
-
(2006)
J Proteome Res
, vol.5
, pp. 695-700
-
-
Klammer, A.A.1
Maccoss, M.J.2
-
17
-
-
15744363160
-
Factors that contribute to the complexity of protein digests
-
Hunyadi-Gulyas, E. and Medzihradszky, K. (2004) Factors that contribute to the complexity of protein digests. DDT Targets, 3, 3–10.
-
(2004)
DDT Targets
, vol.3
, pp. 3-10
-
-
Hunyadi-Gulyas, E.1
Medzihradszky, K.2
-
18
-
-
27544511899
-
InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
-
Tanner, S., Shu, H., Frank, A., Wang, L., Zandi, E., Mumby, M., Pevzner, P., and Bafna, V. (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem, 77, 4626–4639.
-
(2005)
Anal Chem
, vol.77
, pp. 4626-4639
-
-
Tanner, S.1
Shu, H.2
Frank, A.3
Wang, L.4
Zandi, E.5
Mumby, M.6
Pevzner, P.7
Bafna, V.8
-
19
-
-
28644447919
-
Identification of post-translational modifications by blind search of mass spectra
-
Tsur, D., Tanner, S., Zandi, E., Bafna, V., and Pevzner, P. A. (2005) Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol, 23, 1562–1567.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1562-1567
-
-
Tsur, D.1
Tanner, S.2
Zandi, E.3
Bafna, V.4
Pevzner, P.A.5
-
20
-
-
33750142707
-
Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility?
-
Wilmarth, P. A., Tanner, S., Dasari, S., Nagalla, S. R., Riviere, M. A., Bafna, V., Pevzner, P. A., and David, L. L. (2006) Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility? J Proteome Res, 5, 2554–2566.
-
(2006)
J Proteome Res
, vol.5
, pp. 2554-2566
-
-
Wilmarth, P.A.1
Tanner, S.2
Dasari, S.3
Nagalla, S.R.4
Riviere, M.A.5
Bafna, V.6
Pevzner, P.A.7
David, L.L.8
-
21
-
-
0019887799
-
Identification of common molecular subse-quences
-
Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subse-quences. J Mol Biol, 147(1), 195–197.
-
(1981)
J Mol Biol
, vol.147
, Issue.1
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
22
-
-
0034915775
-
Mutation-tolerant protein identification by mass spectrometry
-
Pevzner, P., Dancík, V., and Tang, C. (2000) Mutation-tolerant protein identification by mass spectrometry. J Comput Biol, 7, 777–787
-
(2000)
J Comput Biol
, vol.7
, pp. 777-787
-
-
Pevzner, P.1
Dancík, V.2
Tang, C.3
-
23
-
-
85139019717
-
-
Springer, Germany
-
Bandeira, N., Tsur, D., Frank, A., and Pevzner, P. (2006) A New Approach to Protein Identification. Apostolico, A., Guerra, C., Istrail, S., Pevzner, P. A., and Waterman, M. (eds.), Proceeding of the Tenth Annual 21 International Conference in Research in Computational Molecular Biology (RECOMB 2006), vol. 3909 of Lecture Notes in Computer Science, pp. 363–378, Springer, Germany.
-
(2006)
Vol. 3909 of Lecture Notes in Computer Science
, pp. 363-378
-
-
-
24
-
-
0037026512
-
Immunology: The roots of antibody diversity
-
Gearhart, P. J. (2002) Immunology: the roots of antibody diversity. Nature, 419, 29–31.
-
(2002)
Nature
, vol.419
, pp. 29-31
-
-
Gearhart, P.J.1
-
26
-
-
33745192259
-
Recombinant poly-clonal antibodies: The next generation of antibody therapeutics?
-
Haurum, J. S. (2006) Recombinant poly-clonal antibodies: the next generation of antibody therapeutics? Drug Discov Today, 11, 655–660.
-
(2006)
Drug Discov Today
, vol.11
, pp. 655-660
-
-
Haurum, J.S.1
-
27
-
-
0242331757
-
Therapeutic potential of venom peptides
-
Lewis, R. J. and Garcia, M. L. (2003) Therapeutic potential of venom peptides. Nat Rev Drug Discov, 2, 790–802.
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 790-802
-
-
Lewis, R.J.1
Garcia, M.L.2
-
28
-
-
28044453535
-
Small peptides, big world: Biotechnological potential in neglected bioactive peptides from arthropod venoms
-
Pimenta, A. M. and De Lima, M. E. (2005) Small peptides, big world: biotechnological potential in neglected bioactive peptides from arthropod venoms. J Pept Sci, 11, 670–676.
-
(2005)
J Pept Sci
, vol.11
, pp. 670-676
-
-
Pimenta, A.M.1
de Lima, M.E.2
-
29
-
-
9444231642
-
Snake venom prothrombin activators similar to blood coagulation factor Xa
-
Joseph, J. and Kini, R. (2004) Snake venom prothrombin activators similar to blood coagulation factor Xa. Curr Drug Targets Cardiovasc Haematol Disord, 4, 397–416.
-
(2004)
Curr Drug Targets Cardiovasc Haematol Disord
, vol.4
, pp. 397-416
-
-
Joseph, J.1
Kini, R.2
-
30
-
-
9444281936
-
Alpha-fibrinogenases
-
Swenson, S., Toombs, C., Pena, L., Johansson, J., and Markland, F.(2004) Alpha-fibrinogenases. Curr Drug Targets Cardiovasc Haematol Disord, 4, 417–435.
-
(2004)
Curr Drug Targets Cardiovasc Haematol Disord
, vol.4
, pp. 417-435
-
-
Swenson, S.1
Toombs, C.2
Pena, L.3
Johansson, J.4
Markland, F.5
-
31
-
-
0035742118
-
Procoagulant proteins from snake venoms
-
Kini, R., Rao, V., and Joseph, J. (2001) Procoagulant proteins from snake venoms. Haemostasis, 31, 218–224.
-
(2001)
Haemostasis
, vol.31
, pp. 218-224
-
-
Kini, R.1
Rao, V.2
Joseph, J.3
-
32
-
-
4444329286
-
Intravenous liposomal delivery of the snake venom disintegrin con-tortrostatin limits breast cancer progression
-
Swenson, S., Costa, F., Minea, R., Sherwin, R., Ernst, W., Fujii, G., Yang, D., and Markland, F. (2004) Intravenous liposomal delivery of the snake venom disintegrin con-tortrostatin limits breast cancer progression. Mol Cancer Ther, 3, 499–511.
-
(2004)
Mol Cancer Ther
, vol.3
, pp. 499-511
-
-
Swenson, S.1
Costa, F.2
Minea, R.3
Sherwin, R.4
Ernst, W.5
Fujii, G.6
Yang, D.7
Markland, F.8
-
33
-
-
0036896057
-
Snake venom as therapeutic agents: From toxin to drug development
-
Pal, S. K., Gomes, A., Dasgupta, S. C., and Gomes, A. (2002) Snake venom as therapeutic agents: from toxin to drug development. Indian J Exp Biol, 40, 1353–1358.
-
(2002)
Indian J Exp Biol
, vol.40
, pp. 1353-1358
-
-
Pal, S.K.1
Gomes, A.2
Dasgupta, S.C.3
Gomes, A.4
-
34
-
-
0035742117
-
A novel snake venom disintegrin that inhibits human ovarian cancer dissemination and angiogenesis in an orthotopic nude mouse model
-
Markland, F., Shieh, K., Zhou, Q., Golubkov, V., Sherwin, R., Richters, V., and Sposto, R. (2001) A novel snake venom disintegrin that inhibits human ovarian cancer dissemination and angiogenesis in an orthotopic nude mouse model. Haemostasis, 31, 183–191.
-
(2001)
Haemostasis
, vol.31
, pp. 183-191
-
-
Markland, F.1
Shieh, K.2
Zhou, Q.3
Golubkov, V.4
Sherwin, R.5
Richters, V.6
Sposto, R.7
-
35
-
-
33644679415
-
Amino acid sequence and biological activity of a gamma-conotoxin-like peptide from the worm-hunt-ing snail Conus austini
-
Zugasti-Cruz, A., Maillo, M., López-Vera, E., Falcón, A., Heimer de la Cotera, E. P., Olivera, B. M., and Aguilar, M. B. (2006) Amino acid sequence and biological activity of a gamma-conotoxin-like peptide from the worm-hunt-ing snail Conus austini. Peptides, 27, 506–511.
-
(2006)
Peptides
, vol.27
, pp. 506-511
-
-
Zugasti-Cruz, A.1
Maillo, M.2
López-Vera, E.3
Falcón, A.4
Heimer de la Cotera, E.P.5
Olivera, B.M.6
Aguilar, M.B.7
-
36
-
-
3343003779
-
Complete amino acid sequence and phylogenetic analysis of a long-chain neurotoxin from the venom of the African banded water cobra, Boulengerina annulata
-
Ogawa, Y., Yanoshita, R., Kuch, U., Samejima, Y., and Mebs, D. (2004) Complete amino acid sequence and phylogenetic analysis of a long-chain neurotoxin from the venom of the African banded water cobra, Boulengerina annulata. Toxicon, 43, 855–858.
-
(2004)
Toxicon
, vol.43
, pp. 855-858
-
-
Ogawa, Y.1
Yanoshita, R.2
Kuch, U.3
Samejima, Y.4
Mebs, D.5
-
37
-
-
0023143159
-
The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry
-
Johnson, R. and Biemann, K. (1987) The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry. Biochemistry, 26, 1209–1214.
-
(1987)
Biochemistry
, vol.26
, pp. 1209-1214
-
-
Johnson, R.1
Biemann, K.2
-
38
-
-
33646059903
-
De novo proteomic sequencing of a monoclonal antibody raised against ox40 ligand
-
Pham, V., Henzel, W. J., Arnott, D., Hymowitz, S., Sandoval, W. N., Truong, B. T., Lowman, H., and Lill, J. R. (2006) De novo proteomic sequencing of a monoclonal antibody raised against ox40 ligand. Anal Biochem, 352, 77–86.
-
(2006)
Anal Biochem
, vol.352
, pp. 77-86
-
-
Pham, V.1
Henzel, W.J.2
Arnott, D.3
Hymowitz, S.4
Sandoval, W.N.5
Truong, B.T.6
Lowman, H.7
Lill, J.R.8
-
39
-
-
34249780156
-
Shotgun protein sequencing
-
Bandeira, N., Clauser, K., and Pevzner, P. (2007) Shotgun protein sequencing: assembly of tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics, 6, 1123–1134.
-
(2007)
Assembly of Tandem Mass Spectra from Mixtures of Modified Proteins. Mol Cell Proteomics
, vol.6
, pp. 1123-1134
-
-
Bandeira, N.1
Clauser, K.2
Pevzner, P.3
-
40
-
-
22544465253
-
Spider: Software for protein identification from sequence tags with de novo sequencing error
-
Han, Y., Ma, B., and Zhang, K. (2005) Spider: software for protein identification from sequence tags with de novo sequencing error. J Bioinform Comput Biol, 3, 697–716.
-
(2005)
J Bioinform Comput Biol
, vol.3
, pp. 697-716
-
-
Han, Y.1
Ma, B.2
Zhang, K.3
-
41
-
-
33646903914
-
Modificomb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures
-
Savitski, M. M., Nielsen, M. L., and Zubarev, R. A. (2006) Modificomb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol Cell Proteomics, 5, 935–948.
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 935-948
-
-
Savitski, M.M.1
Nielsen, M.L.2
Zubarev, R.A.3
-
42
-
-
0035107717
-
Efficiency of database search for identification of mutated and modified proteins via mass spectrometry
-
Pevzner, P., Mulyukov, Z., Dancik, V., and Tang, C. (2001) Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res, 11, 290–299.
-
(2001)
Genome Res
, vol.11
, pp. 290-299
-
-
Pevzner, P.1
Mulyukov, Z.2
Dancik, V.3
Tang, C.4
-
43
-
-
2442621619
-
Discovery and development of bevacizumab, an anti-vegf antibody for treating cancer
-
Ferrara, N., Hillan, K. J., Gerber, H. P., and Novotny, W. (2004) Discovery and development of bevacizumab, an anti-vegf antibody for treating cancer. Nat Rev Drug Discov, 3, 391–400.
-
(2004)
Nat Rev Drug Discov
, vol.3
, pp. 391-400
-
-
Ferrara, N.1
Hillan, K.J.2
Gerber, H.P.3
Novotny, W.4
-
44
-
-
34247876138
-
Development trends for monoclonal antibody cancer therapeutics
-
Reichert, J. M. and Valge-Archer, V. E. (2007) Development trends for monoclonal antibody cancer therapeutics. Nat Rev Drug Discov, 6, 349–356.
-
(2007)
Nat Rev Drug Discov
, vol.6
, pp. 349-356
-
-
Reichert, J.M.1
Valge-Archer, V.E.2
-
45
-
-
57449097186
-
Automated de novo protein sequencing of monoclonal antibodies
-
Bandeira, N., Pham, V., Pevzner, P., Arnott, D., and Lill, J.R. (2008) Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol, 26, 1336–1338.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1336-1338
-
-
Bandeira, N.1
Pham, V.2
Pevzner, P.3
Arnott, D.4
Lill, J.R.5
-
46
-
-
24044508863
-
New data base-independent, sequence tag-based scoring of peptide ms/ms data validates mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of ms/ms techniques
-
Savitski, M. M., Nielsen, M. L., and Zubarev, R. A. (2005) New data base-independent, sequence tag-based scoring of peptide ms/ms data validates mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of ms/ms techniques. Mol Cell Proteomics, 4, 1180–1188.
-
(2005)
Mol Cell Proteomics
, vol.4
, pp. 1180-1188
-
-
Savitski, M.M.1
Nielsen, M.L.2
Zubarev, R.A.3
-
47
-
-
29144437803
-
Proteomics-grade de novo sequencing approach
-
Savitski, M. M., Nielsen, M. L., Kjeldsen, F., and Zubarev, R. A. (2005) Proteomics-grade de novo sequencing approach. J Proteome Res, 4, 2348–2354.
-
(2005)
J Proteome Res
, vol.4
, pp. 2348-2354
-
-
Savitski, M.M.1
Nielsen, M.L.2
Kjeldsen, F.3
Zubarev, R.A.4
-
48
-
-
33846600820
-
De novo peptide sequencing and identification with precision mass spectrometry
-
Frank, A. M., Savitski, M. M., Nielsen, M. L., Zubarev, R. A., and Pevzner, P. A. (2007) De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res, 6, 114–123.
-
(2007)
J Proteome Res
, vol.6
, pp. 114-123
-
-
Frank, A.M.1
Savitski, M.M.2
Nielsen, M.L.3
Zubarev, R.A.4
Pevzner, P.A.5
-
49
-
-
0030960366
-
Rapid “de novo” peptide sequencing by a combination of nanoelectro-spray, isotopic labeling and a quadrupole/ time-of-flight mass spectrometer
-
Shevchenko, A., Chernushevich, I., Ens, W., Standing, K. G., Thomson, B., Wilm, M., and Mann, M. (1997) Rapid “de novo” peptide sequencing by a combination of nanoelectro-spray, isotopic labeling and a quadrupole/ time-of-flight mass spectrometer. Rapid Commun Mass Spectrom, 11, 1015–1024.
-
(1997)
Rapid Commun Mass Spectrom
, vol.11
, pp. 1015-1024
-
-
Shevchenko, A.1
Chernushevich, I.2
Ens, W.3
Standing, K.G.4
Thomson, B.5
Wilm, M.6
Mann, M.7
-
50
-
-
0029105096
-
Molecular cloning and expression of catrocollastatin, a snake-venom protein from Crotalus atrox (western diamondback rattlesnake) which inhibits platelet adhesion to collagen
-
Zhou, Q., Smith, J. B., and Grossman, M. H. (1995) Molecular cloning and expression of catrocollastatin, a snake-venom protein from Crotalus atrox (western diamondback rattlesnake) which inhibits platelet adhesion to collagen. Biochem J, 307(Pt 2), 411–417.
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(1995)
Biochem J
, vol.307
, Issue.2
, pp. 411-417
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Zhou, Q.1
Smith, J.B.2
Grossman, M.H.3
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