[1] D. Figeys, Proteomics approaches in drug discovery, Anal. Chem., 74 (2004) 413A-419A.
[2] G.C. Terstappen, A. Reggiani, In silico research in drug discovery, Trends Pharm. Sci., 22 (2001) 23-26.
[3] J. Drews, Genomic sciences and the medicine of tomorrow, Nat. Biotechnol., 14 (1996) 1516-1518.
[4] J. Drews, S. Ryser, The role of innovation in drug development, Nat. Biotechnol., 15 (1997) 1318-1319.
[5] S. Grabley, R. Thiericke (red.), Drug Discovery from Nature, Springer-Verlag, Berlin, 1999.
[6] A. Abbott, A post-genomic challenge: learning to read patterns of protein synthesis, Nature, 402 (1999) 715-720.
[7] K.A. Cole, D.B. Krizman, M.R. Emmert-Buck, The genetics of cancer – a 3D model, Nat. Genet. Suppl., 21 (1999) 38-41.
[8] T. Bączek, Proteomika a nowotwory, Farmacja Polska, 62 (2006) 12-19.
[9] J.L. Walgren, D.C. Thompson, Application of proteomic technologies in the drug de-velopment process, Toxicol. Lett., 149 (2004) 377-385.
[10] G. Stix, Parsing cells, Sci. Am., 281 (1999) 35-36.
[11] T. Bączek, R. Kaliszan, Nowoczesne techniki analityczne w proteomice, w: Miniatury-zacja w analityce (red. Z. Brzózka), Oficyna Wydawnicza Politechniki Warszawskiej, Warszawa, 2005.
[12] M.R. Wilkins, J.C. Sanchez, A.A. Gooley, R.D. Appel, I. Humphery-Smith, D.F.
Hochstrasser, K.L. Williams, Progress with proteome projects: why all proteins ex-pressed by a genome should be identified and how to do it, Biotechnol. Genet. Eng.
Rev., 13 (1996) 41-50.
[13] V.C. Wasinger, G.L. Corthals, Proteomic tools for biomedicine, J. Chromatogr. B, 771 (2002) 33-49.
[14] S. Fields, Proteomics in genomeland, Science, 291 (2001) 1221-1224.
[15] D.C. Liebler, Introduction to Proteomics, Humana Press, Totowa, NJ, 2002.
[16] International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome, Nature, 409 (2001) 860-921.
[17] J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural et al., The sequence of the human genome, Science, 291 (2001) 1304-1351.
[18] F.S. Collins, E.S. Lander, J. Rogers, R.H. Waterson, Finishing the euchromatic se-quence of the human genome, Nature, 431 (2004) 931-945.
[19] A. Pandey, M. Mann, Proteomics to study genes and genomes, Nature, 405 (2000) 837-846.
[20] M. Caron, N. Imam-Sghiouar, F. Poirier, J-.P. Le Caër, V. Labas, Raymonde Joubert-Caron, Proteomic map and database of lymphoblastoid proteins, J. Chromatogr. B, 771 (2002) 197-209.
[21] T. Nakanishi, R. Koyama, T. Ikeda, A. Shimizu, Catalogue of soluble proteins in the human vitreous humor: comparison between diabetic retinopathy and macular hole, J.
Chromatogr. B, 776 (2002) 89-100.
[22] I. Noël-Georis, A. Bernard, P. Falmagne, R. Wattiez, Database of bronchoalveolar lav-age fluid proteins, J. Chromatogr. B, 771 (2002) 221-236.
[23] A. Sickmann, W. Dormeyer, S. Wortelkamp, D. Woitalla, W. Kuhn, H.E. Meyer, To-wards a high resolution separation of human cerebrospinal fluid, J. Chromatogr. B, 771 (2002) 167-196.
[24] M.J. Hubbard, J.C. Kon, Proteomic analysis of dental tissues, J. Chromatogr. B, 771 (2002) 211-220.
[25] N.L. Anderson, N.G. Anderson, The human plasma proteome, Mol. Cell Proteomics, 1 (2002) 845-867.
[26] J.N. Adkins, S.M. Varnum, K.J. Auberry, R.J. Moore, N.H. Angell, R.D. Smith, D.I.
Springer, J.G. Pounds, Toward a human blood serum proteome: analysis by multidi-mensional separation coupled with mass spectrometry, Mol. Cell Proteomics, 1 (2002) 947-955.
[27] M. Tichá, V. Pacáková, K. Stulik, Proteomics of allergens, J. Chromatogr. B, 771 (2002) 343-353.
[28] R. Kellner, F. Lottspeich, H.E. Meyer, Microcharacterization of Proteins, Wiley-VCH, Weinheim, 1999.
[29] T. Wehr, Separation technology in proteomics, LCGC North America, 19 (2001) 702-711.
[30] T. Rabilloud, Two-dimensional gel elctrophoresis in proteomics: old, old fashioned, but still climbs up the mountains, Proteomics, 2 (2002) 3-10.
[31] P.G. Righetti, A. Castagna, B. Herbert, Prefractionation techniques in proteome analy-sis, Anal. Chem., 73 (2001) 320A-326A.
[32] P.G. Righetti, A.V. Stoyanov, M.Y. Zhukov, The Proteome Revisited. Theory and Practice of All Relevant Electrophoretic Steps, Elsevier, Amsterdam, 2001.
[33] D. Jäger, P.R. Jungblut, U. Müller-Werdan, Separation and identification of human heart proteins, J. Chromatogr. B, 771 (2002) 131-153.
[34] R.C.M.Y. Liang, J.C.H. Neo, S.L. Lo, G.S. Tan, T.K. Seow, M.C.M. Chung, Proteome database of hepatocellular carcinoma, J. Chromatogr. B, 771 (2002) 303-328.
[35] B. Herbert, P.G. Righetti, A turning point in proteome analysis: sample prefractionation via multicompartment electrolyzer with isoelectric membranes, Electrophoresis, 21 (2000) 3639-3648.
[36] X. Zuo, P. Hembach, L. Echan, D.W. Speicher, Enhanced analysis of human breast cancer proteomes using micro-scale solution isoelectrofocusing combined with high resolution 1-D and 2-D gels, J. Chromatogr., 782 (2002) 253-265.
[37] A. Tan, A. Pashkova, L. Zang, F. Foret, B.L. Karger, A miniaturized multichamber solution isoelectric focusing device for separation of protein digests, Electrophoresis, 23 (2002) 3599-3607.
[38] T. Bączek, Fractionation of peptides in proteomics with the use of pI-based approach and ZipTip pipette tips, J. Pharm. Biomed. Anal., 34 (2004) 851-860.
[39] T. Bączek, Fractionation of peptides and identification of proteins from Saccharomyces cerevisiae in proteomics with the use of reversed-phase capillary liquid chromatogra-phy and pI-based approach, J. Pharm. Biomed. Anal., 35 (2004) 895-904.
[40] T. Bączek, A. Buciński, A.R. Ivanov, R. Kaliszan, Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics, Anal. Chem., 76 (2004) 1726-1732.
[41] R. Kaliszan, T. Bączek, A. Cimochowska, P. Juszczyk, K. Wiśniewska, Z. Grzonka, Prediction of high-performance liquid chromatography retention of peptides with the use of quantitative structure-retention relationships, Proteomics, 5 (2005) 409-415.
[42] T. Bączek, P. Wiczling, M. Marszałł, Y. Vander Heyden, R. Kaliszan, Prediction of peptide retention at different HPLC conditions from multiple linear regression models, J. Proteome Res., 4 (2005) 555-563.
[43] T. Bączek, Chemometric evaluation of relationships between retention and physico-chemical parameters in terms of multidimensional liquid chromatography of peptides, J. Sep. Sci., 29 (2006) 547-554.
[44] R. Put, M. Daszykowski, T. Bączek, Y. Vander Heyden, Retention prediction of pep-tides based on uninformative variable elimination by partial least squares, J. Proteome Res., 5 (2006) 1618-1625.
[45] S.-L. Wu, H. Amato, R. Biringer, G. Choudhary, P. Shieh, W.S. Hancock, Targeted proteomics of low-level proteins in human plasma by LC/MSn: using human growth hormone as a model system, J. Proteome Research, 1 (2002) 459-465.
[46] A. Premstaller, H. Oberacher, W. Walcher, A.M. Timperio, L. Zolla, J.-P. Chervet, N.
Cavusoglu, A. van Dorsselaer, C.G. Huber, High-performance liquid chromatography-electophoresis ionization mass spectrometry using monolithic capillary columns for proteomics studies, Anal. Chem., 73 (2001) 2390-2396.
[47] L.J. Licklider, C.C. Thoreen, J. Peng, S.P. Gygi, Automation of nanoscale microcapil-lary liquid chromatography-tandem mass spectrometry with a vented column, Anal.
Chem., 74 (2002) 3076-3083.
[48] J. Preisler, P. Hu, T. Rejtar, B.L. Karger, Capillary electrophoresis – matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a vacuum deposition interface, Anal. Chem., 72 (2000) 4785-4795.
[49] B. Zhang, F. Foret, B.L. Karger, High-throughput microfabricated CE/ESI-MS: auto-mated sampling from a microwell plate, Anal. Chem., 73 (2001) 2675-2681.
[50] M. Minarik, K. Klepàrnik, M. Gilàr, F. Foret, A.W. Miller, Z. Sosic, B.L. Karger, De-sign of a fraction collector for capillary array electrophoresis, Electrophoresis, 23 (2002) 35-42.
[51] R. Joubert, J.-M. Strub, S. Zugmeyer, D. Kobi, N. Carte, A. van Dorsselaer, H.
Boucherie, L. Jaquet-Gutfreund, Identification by mass spectrometry of two-dimensional gel electrophoresis-separated proteins extracted from lager brewing yeast, Electrophoresis, 22 (2001) 2969-2982.
[52] M. Perrot, F. Sagliocco, T. Mini, C. Monribot, U. Schneider, A. Shevchenko, M. Mann, P. Jeno, H. Boucherie, Two-dimensional gel protein database of Saccharomyces cere-visiae (update 1999), Electrophoresis, 20 (1999) 2280-2298.
[53] M. Poutanen, L. Salusjarvi, L. Ruohonen, M. Penttila, N. Kalkkinen, Use of matrix-assisted laser desorption/ionization time-of-flight mass mapping and nanospray liquid
chromatography/electrospray ionization tandem mass spectrometry sequence tag analy-sis for sensitive, Rapid Commun. Mass Spectrom., 15 (2001) 1685-1692.
[54] L. Salusjarvi, M. Poutanen, J.-P. Pitkanen, H. Koivistoinen, A. Aristidou, N. Kalkkinen, L. Ruohonen, M. Penttila, Proteome analysis of recombinant xylose-fermenting Sac-charomyces cerevisiae, Yeast, 20 (2003) 295-314.
[55] D.M. Lubman, M.T. Kachman, H. Wang, S. Gong, F. Yan, R.L. Hamler, K.A. O’Neil, K. Zhu, N.S. Buchanan, T.J. Barder, Two-dimensional liquid separations–mass map-ping of proteins from human cancer cell lysates, J. Chromatogr. B, 782 (2002) 183-196.
[56] A. Ros, M. Faupel, H. Mees, J. Van Oostrum, R. Ferrigno, F. Reymond, P. Michel, J.S.
Rossier, H.H. Girault, Protein purification by off-gel electrophoresis, Proteomics, 2 (2002) 151-156.
[57] M. Cretich, G. Pirri, G. Carrea, M. Chiari, Separation of proteins in a multicompart-ment electrolyzer with chambers defined by a bed of gel beads, Electrophoresis, 24 (2003) 577-581.
[58] X. Kang, D.D. Frey, Chromatofocusing using micropellicular column packings with com-puter-aided design of the elution buffer composition, Anal. Chem., 74 (2002) 1038-1045.
[59] Y. Shen, F. Xiang, T.D. Veenstra, E.N. Fung, R.D. Smith, High-resolution capillary isoelectric focusing of complex protein mixtures from lysates of microorganisms, Anal.
Chem., 71 (1999) 5348-5353.
[60] Y. Shen, S.J. Berger, G.A. Anderson, R.D. Smith, High-efficiency capillary isoelectric focusing of peptides, Anal. Chem., 72 (2000) 2154-2159.
[61] L.R. Snyder, J.J. Kirkland, J.L. Glajch, Practical HPLC Method Development, John Wiley & Sons, New York, 1997.
[62] J. Swadesh, HPLC Practical and Industrial Applications, CRC Press, Boca Raton, 1997.
[63] R. Kaliszan, Structure and Retention in Chromatography. A Chemometric Approach, Harwood Academic Publishers, Amsterdam, 1997.
[64] S.R. Pennington, M.J. Dunn (red.), Proteomics. From Protein Sequence to Function.
BIOS Scientific Publishers, Springer-Verlag, New York, 2001.
[65] http://eugenes.org:7072/
[66] J. Peng, J.E. Elias, C.C. Thoreen, L.J. Licklider, S.P. Gygi, Evaluation of multidimen-sional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome, J. Proteome Res., 2 (2003) 43- 50.
[67] H.J. Cortes, Multidimensional Chromatography. Techniques and Applications, Marcel Dekker, New York, 1990.
[68] F. Regnier, A. Amini, A. Chakraborty, M. Geng, J. Ji, L. Riggs, C. Sioma, S. Wang, X.
Zhang, Multidimensional chromatography and the signature peptide approach to pro-teomics, LCGC North America, 19 (2001) 200-213.
[69] T. Wehr, Multidimensional liquid chromatography in proteomic studies, LCGC North America, 20 (2002) 954-962.
[70] S.P. Gygi, B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, R. Aebersold, Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotech-nol., 17 (1999) 994-999.
[71] S.P. Gygi, B. Rist, T.J. Griffin, J. Eng, R. Aebersold, Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags, J. Proteome Res., 1 (2002) 47-54.
[72] A.J. Link, J. Eng, D.M. Schieltz, E. Carmack, G.J. Mize, D.R. Morris, B.M. Garvik, J.R. Yates III, Direct analysis of protein complexes using mass spectrometry, Nat. Bio-technol., 17 (1999) 676-682.
[73] M.P. Washburn, D. Wolters, J.R. Yates III, Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Nat. Biotechnol., 19 (2001) 242-247.
[74] M.P. Washburn, R. Ulaszek, C. Deciu, D.M. Schieltz, J.R. Yates III, Analysis of quan-titative proteomic data generated via multidimensional protein identification technol-ogy, Anal. Chem., 74 (2002) 1650-1657.
[75] G.J. Opiteck, K.C. Lewis, J.W. Jorgenson, R.J. Anderegg, Comprehensive on-line LC/LC/MS of proteins, Anal. Chem., 69 (1997) 1518-1524.
[76] K. Wagner, T. Miliotis, G. Marko-Varga, R. Bischoff, K.K. Unger, An automated on-line multidimensional HPLC system for protein and peptide mapping with integrated sample preparation, Anal. Chem., 74 (2002) 809-820.
[77] J.T. Watson, Introduction to Mass Spectrometry, Lippincott-Raven, Philadelphia, PA, 1997.
[78] T. Bączek, Techniki rozdzielcze i spektrometria masowa w badaniach ludzkiego prote-omu. Proteomika – nowe narzędzie w naukach medyczno-farmaceutycznych, Farmacja Polska, 59 (2003) 204-213.
[79] J.R. Yates III, Mass spectrometry and the age of the proteome, J. Mass Spectrom., 33 (1998) 1-19.
[80] R.M. Caprioli, A. Malorni, G. Sindona, Selected Topics in Mass Spectrometry in the Biomolecular Sciences, Kluwer Academic Publishers, Dordrecht, 1997.
[81] http://www.ebi.uniprot.org/index.shtml
[87] D.N. Perkins, D.J.C. Pappin, D.M. Creasy, J.S. Cottrell, Probability-based protein iden-tification by searching databases using mass spectrometry data, Electrophoresis, 20 (1999) 3551-3567.
[88] J. Mazerski, Podstawy chemometrii, Wydawnictwo Politechniki Gdańskiej, Gdańsk, 2000.
[89] J.K. Eng, A.L. McCormack, J.R. Yates III, An approach to correlate tandem mass spec-tral data of peptides with amino acid sequences in a protein database, J. Am. Soc. Mass Spectrom., 5 (1994) 976-989.
[90] J.R. Yates, III, J.K. Eng, A.L. McCormack, D. Schieltz, Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database, Anal. Chem., 67 (1995) 1426-1436.
[91] D.C. Anderson, W. Li, D.G. Payan, W.S. Noble, A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores, J. Proteome Res., 2 (2003) 137-146.
[92] D.L. Tabb, W.H. McDonald, J.R. Yates, III, DTASelect and Contrast: tools for assem-bling and comparing protein identifications from shotgun proteomics, J. Proteome Res., 1 (2002) 2-26.
[93] J. Zupan, J. Gasteiger, Neural networks: A new method for solving chemical problems or just a passing phase?, Anal. Chim. Acta, 248 (1991) 1-30.
[94] J. Zupan, J. Gasteiger, Neural Networks for Chemists. An Introduction, VCH, Weinhe-im, 1993.
[95] K. Petritis, L.J. Kangas, P.L. Ferguson, G.A. Anderson, L. Pasa-Tolic, M.S. Lipton, K.J. Auberry, E.F. Strittmatter, Y. Shen, R. Zhao, R.D. Smith, Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses, Anal. Chem., 75 (2003) 1039-1048.
[96] J.L. Meek, Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition, Proc. Natl. Acad. Sci, USA, 77 (1980) 1632-1636.
[97] C.A. Browne, H.P.J. Bennett, S. Solomon, The isolation of peptides by high-performance liquid chromatography using predicted elution positions, Anal. Biochem., 124 (1982) 201-208.
[98] V. Casal, P.J. Martin-Alvarez, T. Herraiz, Comparative prediction of the retention be-haviour of small peptides in several reversed-phase high-performance liquid chroma-tography columns by using partial least squares and multiple linear regression, Anal.
Chim. Acta, 326 (1996) 77-84.
[99] D. Guo, C.T. Mant, A.K. Taneja, J.M.R. Parker, R.S. Hodges, Prediction of peptide retention times in reversed-phase high-performance liquid chromatography. I. Determi-nation of retention coefficients of amino acid residues of model synthetic peptides, J.
Chromatogr., 359 (1986) 499-518.
[100] D. Guo, C.T. Mant, A.K. Taneja, R.S. Hodges, Prediction of peptide retention times in reversed-phase high-performance liquid chromatography. II. Correlation of observed and predicted peptide retention times and factors influencing the retention times of pep-tides, J. Chromatogr., 359 (1986) 519-532.
[101] C.T. Mant, N.E. Zhou, R.S. Hodges, Correlation of protein retention times in reversed-phase chromatography with polypeptide chain length and hydrophobicity, J. Chroma-togr., 476 (1989) 363-375.
[102] R.A. Houghten, S.T. DeGraw, Effect of positional environmental domains on the varia-tion of high-performance liquid chromatographic peptide retenvaria-tion coefficients, J.
Chromatogr., 386 (1987) 223-228.
[103] N.E. Zhou, C.T. Mant, R.S. Hodges, Effect of preferred binding domains on peptide retention behavior in reversed-phase chromatography: amphipathic alpha-helices, Pept.
Res., 3 (1990) 8-20.
[104] M. Palmblad, M. Ramström, K.E. Markides, P. Håkansson, J. Bergquist, Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry, Anal. Chem., 74 (2002) 5826-5830.
[105] M. Palmblad, M. Ramström, C.G. Bailey, S.L. McCutchen-Maloney, J. Bergquist, L.C.
Zeller, Protein identification by liquid chromatography mass spectrometry using reten-tion time predicreten-tion, J. Chromatogr. B, 803 (2004) 131-135.
[106] R. Kaliszan, Quantitative Structure-Chromatographic Retention Relationships, Wiley, New York, 1987.
[107] A. Kraj, J. Silberring (red.), Proteomika, Wydział Chemii Uniwersytetu Jagiellońskie-go, Kraków, 2004.
[108] T. Bączek, R. Kaliszan, Proteomika a techniki separacyjne, Farmacja Polska, 57 (2001) 923-925.
[109] T. Bączek, Improvement of peptides identification in proteomics with the use of new analytical and bioinformatic strategies, Curr. Pharm. Anal., 1 (2005) 31-40.