Journal : Acta Chromatographica
Article : Identification of peptides in proteomics supported by prediction of peptide retention by means of quantitative structure-retention relationships

Authors :
Bartnik, M.
Department of Pharmacognosy with Medicinal Plant Laboratory, Medical University, 1, Chodźki Str., 20-093 Lublin, Poland,
Kowalski, R.
Subdepartment of Food Quality Assessment and Central Apparatus Laboratory, Agricultural University, 20-950 Lublin, Akademicka 13, Poland,
Polak, B.
Department of Physical Chemistry, Faculty of Pharmacy, Medical University, Lublin, Poland,
Turło, J.
Department of Drug Technology, Medical University of Warsaw, 1, Banacha Street, 02-097 Warsaw, Poland,
Szyrwińska, K.
Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Poznań University of Medical Sciences, Grunwaldzka 6, 60-780 Poznań, Poland,
Czauderna, M.
The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland,
Bączek, T.
Medical University of Gdańsk, Department of Biopharmaceutics and Pharmacodynamics, Gdańsk, Poland,
Abstract : Quantitative structure-retention relationships (QSRR) have been derived for prediction of RP-HPLC retention of peptides obtained by online digestion of myoglobin. To characterize the structure of a peptide quantitatively, and then to predict its retention time under gradient HPLC conditions, the structural descriptors used were: the logarithm of the sum of retention times of the amino acids of the peptide, log SumAA; the logarithm of the Van der Waals volume of the peptide, log VDWVol; and the logarithm of its calculated n-octanol-water partition coefficient, clog P. The predictive power of the QSRR model was checked by use of a myoglobin digest, after separation and identification of the peptides by LC-ESI-MS-MS. On-line protein digestion was performed by use of trypsin immobilized on an epoxy-modified silica monolithic support coupled on-line to LC-ESIMS -MS. The predicted gradient retention times of the peptides were related to the experimental retention times obtained after on-line digestion of myoglobin. Identification of the components of the protein digest was supported by QSRR analysis. The QSRR approach was used as an additional constraint in proteomic research to verify results from MS-MS ion search, and to confirm both correctness of peptide identifications and indications of potential false positive and false negative results. The results suggest that because of the use of QSRR for prediction of peptide retention, information derived from standard liquid chromatographic separation in proteomics research could also be useful for eventual identification of the peptides.

Keywords :
Publishing house : University of Silesia in Katowice
Publication date : 2007
Number : No. 18
Page : 72 – 92

: 1 R. Kaliszan, T. Bączek, A. Cimochowska, P. Juszczyk, K. Wiśniewska, and Z. Grzonka, Proteomics, 5, 409 (2005)
2 T. Bączek, P. Wiczling, M.P. Marszałł, Y. Vander Heyden, and R. Kaliszan, J. Proteome Res., 4, 555 (2005)
3 J.L. Meek, Proc. Natl. Acad. Sci. USA, 77, 1632 (1980)
4 C.A. Browne, H.P.J. Bennett, and S. Solomon, Anal. Biochem., 124, 201 (1982)
5 V. Casal, P.J. Martin-Alvarez, and T. Herraiz, Anal. Chim. Acta, 326, 77 (1996)
6 D. Guo, C.T. Mant, A.K. Taneja, J.M.R. Parker, and R.S. Hodges, J. Chromatogr., 359, 499 (1986)
7 M. Palmblad, M. Ramström, K.E. Markides, P. Håkansson, and J. Bergquist, Anal. Chem., 74, 5826 (2002)
8 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, and R.D. Smith, Anal. Chem., 75, 1039 (2003)
9 E.F. Strittmatter, L.J. Kangas, K. Petritis, H.M. Mottaz, A.A. Anderson, Y. Shen, J.M. Jacobs, D.G. Camp II, and R.D. Smith, J. Proteome Res., 3, 760 (2004)
10 T. Kawakami, K. Tateishi, K. Yamano, T. Ishikawa, K. Kuroki, and T. Nishimura, Proteomics, 5, 856 (2005)
11 C.T. Mant, N.E. Zhou, and R.S. Hodges, J. Chromatogr., 476, 363 (1989)
12 R. Kaliszan, Quantitative Structure–Chromatographic Retention Relationships, Wiley, New York, 1987
13 R. Kaliszan, J. Chromatogr., 656, 417 (1993)
14 E. Forgacs and T. Cserhati, Molecular Bases of Chromatographic Separations, Boca Raton, CRC Press, 1997
15 R. Kaliszan, M.A. van Straten, M. Markuszewski, C.A. Cramers, and H.A. Claessens, J. Chromatogr. A, 855, 455 (1999)
16 T. Bączek and R. Kaliszan, J. Chromatogr. A, 962, 41 (2002)
17 T. Bączek and R. Kaliszan, J. Chromatogr. A, 987, 29 (2003)
18 R. Kaliszan, T. Bączek, A. Buciński, B. Buszewski, and M. Sztupecka, J. Sep. Sci., 26, 271 (2003)
19 D.N. Perkins, D.J.C. Pappin, D.M. Creasy, and J.S. Cottrell, Electrophoresis, 20, 3551 (1999)
20 J.K. Eng, A.L. McCormack, and J.R. Yates III, J. Am. Soc. Mass Spectrom., 5, 976 (1994)
21 J.R. Yates III, J.K. Eng, A.L. McCormack, and D. Schieltz, Anal. Chem., 67, 1426 (1995)
22 D.C. Anderson, W. Li, D.G. Payan, and W.S. Noble, J. Proteome Res., 2, 137 (2003)
23 D.L. Tabb, W.H. McDonald, and J.R. Yates III, J. Proteome Res., 1, 21 (2002)
24 M.P. Washburn, D. Wolters, and J.R. Yates III, Nat. Biotechnol., 19, 242 (2001)
25 J. Peng, J.E. Elias, C.C. Thoreen, L.J. Licklider, and S.P. Gygi, J. Proteome Res., 2, 43 (2003)
26 L. Florens, M.P. Washburn, J.D. Raine, R.M. Anthony, M. Grainger, J.D. Hayness, J.K. Moch, N. Muster, J.B. Sacci, D.L. Tabb, A.A. Witney, D. Wolters, Y. Wu, M.J. Gardner, A.A. Holder, R.E. Sinden, J. Yates, and D.J. Carucci, Nature, 419, 520 (2002)
27 J.N. Adkins, S.M. Varnum, K.J. Auberry, R.J. Moore, N.H. Angell, R.D. Smith, D.L. Springer, and J.G. Pounds, Mol. Cell. Proteomics, 1, 947 (2002)
28 W.-J. Qian, T. Liu, M.E. Monroe, E.F. Strittmatter, J.M. Jacobs, L.J. Kangas, K. Petritis, D.G. Camp II, and R.D. Smith, J. Proteome Res., 4, 53 (2005)
29 E. Calleri, C. Temporini, E. Perani, C. Stella, S. Rudaz, D. Lubda, G. Mellerio, J.-L. Veuthey, G. Caccialanza, and G. Massolini, J. Chromatogr. A, 1045, 99 (2004)
30 E. Antonini and M. Brunori, Hemoglobin and Myoglobin in their Reactions with Ligands, North Holland Publishing, Amsterdam, 1971
Qute : Bartnik, M. ,Kowalski, R. ,Polak, B. ,Turło, J. ,Szyrwińska, K. ,Czauderna, M. ,Bączek, T. ,Bączek, T. , Identification of peptides in proteomics supported by prediction of peptide retention by means of quantitative structure-retention relationships. Acta Chromatographica No. 18/2007