Abstract
Proteins are commonly identified through enzymatic digestion and generation of short sequence tags or fingerprints of peptide masses by mass spectrometry. Separation methods, such as liquid chromatography and electrophoresis, are often used to fractionate complex protein or peptide mixtures and these separations also provide information on the different species, such as molecular weight and isoelectric point from electrophoresis and hydrophobicity in reversed-phase chromatography. These are also properties that can be predicted from amino acid sequences derived from genomic sequences and used in protein identification. This chapter reviews recently introduced methods based on retention time prediction to extract information from chromatographic separations and the applications to protein identification in organisms with small and large genomes. Novel data on retention time prediction of posttranslationally modified peptides is also presented.
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Klose, J. (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231–243.
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.
Whitehouse, C. M., Dreyer, R. N., Yamashita, M., and Fenn, J. B. (1985) Electrospray interface for liquid chromatographs and mass spectrometers. Anal. Chem. 57, 675–679.
Stacey, C. C., Kruppa, G. H., Watson, C. H., et al. (1994) Reverse-phase liquid chromatography/electrospray-ionization Fourier-transform mass spectrometry in the analysis of peptides. Rapid Commun. Mass Spectrom. 8, 513–516.
Voyksner, R. D. (1997) Combining liquid chromatography with electrospray mass spectrometry, in: Electrospray Ionization Mass Spectrometry, (Cole, R. B., ed.), John Wiley and Sons, New York, pp. 323–341.
Jensen, P. K., Pasa-Tolic, L., Peden, K. K., et al. (2000) Mass spectrometric detection for capillary isoelectric focusing separations of complex protein mixtures. Electrophoresis 21, 1372–1380.
Smith, R. D., Pasa-Tolic, L., Lipton, M. S., et al. (2001) Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry. Electrophoresis 22, 1652–1668.
Shen, Y., Tolic, N., Zhao, R., et al. (2001) High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line highperformance ESI FTICR mass spectrometry. Anal. Chem. 73, 3011–3021.
Conrads, T. P., Alving, K., Veenstra, T. D., et al. (2001) Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal. Chem. 73, 2132–2139.
Smith, R. D., Anderson, G. A., Lipton, M. S., et al. (2002) The use of accurate mass tags for high-throughput microbial proteomics. Omics 6, 61–90.
Frenz, J., Hancock, W. S., Henzel, W. J., and Horváth, C. (1990) Reversed phase chromatography in analytical biotechnology of proteins, in HPLC of Biological Macromolecules: Methods and Applications, (Gooding, M. and Regnier, F. E., ed.), Marcel Dekker, New York, pp. 145–177.
Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A., and DeLisi, C. (1987) Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol. 195, 659–685.
Zubarev, R. A., Håkansson, P., and Sundqvist, B. U. R. (1996) Accuracy requirements for peptide characterization by monoisotopic mass measurements. Anal. Chem. 68, 4060–4063.
Conrads, T. P., Anderson, G. A., Veenstra, T. D., Pasa-Tolic, L., and Smith, R. D. (2000) Utility of accurate mass tags for proteome-wide protein identification. Anal. Chem. 72, 3349–3354.
Bruce, J. E., Anderson, G. A., Wen, J., Harkewicz, R., and Smith, R. D. (1999) High-mass-measurement accuracy and 100% sequence coverage of enzymatically digested bovine serum albumin from an ESI-FTICR mass spectrum. Anal. Chem. 71, 2595–2599.
Palmblad, M., Ramström, M., Markides, K. E., Håkansson, P., and Bergquist, J. (2002) Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry. Anal. Chem. 74, 5826–5830.
Hodges, R. S., Parker, J. M., Mant, C. T., and Sharma, R. R. (1988) Computer simulation of high-performance liquid chromatographic separations of peptide and protein digests for development of size-exclusion, ion-exchange and reversed-phase chromatographic methods. J. Chromatogr. 458, 147–167.
Hearn, M. T., Aguilar, M. I., Mant, C. T., and Hodges, R. S. (1988) High-performance liquid chromatography of amino acids, peptides and proteins. LXXXV. Evaluation of the use of hydrophobicity coefficients for the prediction of peptide elution profiles. J. Chromatogr. 438, 197–210.
Mant, C. T., Zhou, N. E., and Hodges, R. S. (1989) Correlation of protein retention times in reversed-phase chromatography with polypeptide chain length and hydrophobicity. J. Chromatogr. 476, 363–375.
Petritis, K., Kangas, L. J., Ferguson, P. L., et al. (2003) Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. Anal. Chem. 75, 1039–1048.
Strittmatter, E. F., Ferguson, P. L., Tang, K., and Smith, R. D. (2003) Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom. 14, 980–991.
Strittmatter, E. F., Kangas, L. J., Petritis, K., et al. (2004) Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J. Proteome Res. 3, 760–769.
Qian, W. J., Liu, T., Monroe, M. E., et al. (2005) Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J. Proteome Res. 4, 53–62.
Nilsson, S., Ramstrom, M., Palmblad, M., Axelsson, O., and Bergquist, J. (2004) Explorative study of the protein composition of amniotic fluid by liquid chromatography electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. J. Proteome Res. 3, 884–889.
Palmblad, M., Ramstrom, M., Bailey, C. G., McCutchen-Maloney, S. L., Bergquist, J., and Zeller, L. C. (2004) Protein identification by liquid chromatography-mass spectrometry using retention time prediction. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 803, 131–135.
The Cygwin homepage. http://www.cygwin.com. Last accessed 05/26/2006.
Matthiesen, R., Bunkenborg, J., Stensballe, A., Jensen, O. N., Welinder, K. G., and Bauw, G. (2004) Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics 4, 2583–2593.
Finney, G., Merrihew, G., Klammer, A., and MacCoss, M. (2004) Protein False Discovery Rates from MS/MS experiments: Decoy Databases and Normalized Cross-Correlation. 52nd American Society for Mass Spectrometry conference on Mass Spectrometry, May 23–27, 2004 Nashville, TN.
Meek, J. L. (1980) Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition. Proc. Natl. Acad. Sci. USA 77, 1632–1636.
Sanz-Nebot, V., Toro, I., Benavente, F., and Barbosa, J. (2002) pKa values of peptides in aqueous and aqueous-organic media. Prediction of chromatographic and electrophoretic behaviour. J. Chromatogr. A 942, 145–156.
Rost, B. (2001) Review: protein secondary structure prediction continues to rise. J. Struct. Biol. 134, 204–218.
Palmblad, M. (2002) Identification and characterization of peptides and proteins using Fourier transform ion cyclotron resonance mass spectrometry. PhD thesis, 05/17/2002, Uppsala Universitet, Uppsala, Sweden.
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Palmblad, M. (2007). Retention Time Prediction and Protein Identification. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 367. Humana Press. https://doi.org/10.1385/1-59745-275-0:195
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DOI: https://doi.org/10.1385/1-59745-275-0:195
Publisher Name: Humana Press
Print ISBN: 978-1-58829-563-7
Online ISBN: 978-1-59745-275-5
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