Abstract
Genome sequencing projects produce large amounts of information that could be translated into potential protein sequences. Such amounts of material continuously increase protein database sizes. At present, 15 times more protein sequences are available in the SWISS-PROT and TrEMBL databases than 8 years ago in SWISS-PROT. One of the methods of choice for protein identification makes use of specific endoproteolytic cleavage followed by the MALDI-MS analysis of the digested product. Since 1993, when this technique was first demonstrated, the conditions required for a correct identification have changed dramatically. Whilst 4–5 peptides with an accuracy of 2–3 Da were sufficient for a correct identification in 1993, 10–13 peptides with less than 60 ppm mass error are now required for Human and E. coli proteins. This evolution is directly related to the continuous increase of protein database sizes, which causes an increase of the number of false positive matches in identification results. Utilisation of an information complement deduced from the primary protein sequence in the process of identification by peptide mass fingerprints can help to increase confidence in the identification results. In this article, we propose the exchange of labile hydrogen atoms with deuterium atoms. The exchange reaction with optimised techniques has shown an average 95% of hydrogen/deuterium exchange on tryptic peptides. This level of exchange was sufficient to single out one or more peptides from a list of potential candidate proteins due to the dependence of hydrogen/deuterium exchange on the peptide primary structure. This technique also has clear advantages in the identification of small proteins where direct protein identification is impaired by the limited number of endoproteolytic peptides. Then, primary sequence information obtained with this technique could help to identify proteins with high confidence without any expensive tandem mass spectrometer instruments.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
7. References
Acharya, A., Maanjula, B., Murthy, G., & Vithayathil, P. (1977). Int JPeptide Protein Res, 9, 213–219.
Adams, M., Celniker, S., Holt, R., Venter, J., & al., e. (2000). Science, 287, 2185–2191.
Axelsson, J., Naven, T., & Fenyo, D. (2001, 4–6th of April). Paper presented at the From biology to pathology: the proteomics perspective, York, UK.
Bairoch, A., & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic acids research, 28, 45–48.
Bartlet-Jones, M., Jeffrey, W., Hansen, H., & Pappin, D. (1994). Peptide ladder sequencing by MS using a novel volatile degradation reagent. Rapid Commun. Mass Spectrom., 8, 737–742.
Bienvenut, W., Hoogland, C., Greco, A., Heller, M., Gasteiger, E., Appel, R., et al. (2002). Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting. Rapid Commun. Mass Spectrom., 16(6), 616–626.
Bienvenut, W., Sanchez, J., Karmime, A., Rouge, V., Rose, K., Binz, P., et al. (1999). Toward a clinical molecular scanner for proteome research: parallel protein chemical processing before and during western blot. Anal Chem, 71(21), 4800–4807.
Blattner, F., Plunkett, G. r., Bloch, C., Perna, N., Burland, V., Riley, M., et al. (1997). Science, 277, 1453–1474.
Brown, R., & Lennon, J. (1995). Mass resolution improvement by incorporation of pulsed ion extraction in a matrix-assisted laser desorption/ionisation linear time-of-flight mass spectrometer. Anal. Chem, 67, 1988–2003.
Chaurand, P., Luetzenkirchen, F., & Spengler, B. (1999). Peptide and protein identification by MALDI-PSD TOF-MS. J. Am. Soc. Mass Spectrom., 10, 91–103.
Clauser, K., Baker, P., & Burlingame, A. (1999). Anal. Chem., 71, 2076–2084.
Consortium, I. H. G. S. (2001). Initial sequencing and analysis of the human genome. Nature, 409(6822), 860–921.
Engen, J., & Smith, D. (2001). Investigating protein structure and dynamics by hydrogen exchange MS. Anal. Chem., 73, J. Chromatogr. A 256–A265.
Englander, J., Rogero, J., & Englander, S. (1985). Anal. Biochem., 147, 234–.
Englander, S., & Kallenbach, N. (1984). Q. Rev. Biophys., 16, 521.
Falick, A., & Maltby, D. (1989). Anal. Biochem., 182, 165–169.
Figueroa, I., Torres, O., & Russell, D. (1998). Effects of the water content in the sample preparation for MALDI on the mass spectra. Anal. Chem., 70, 4527–4533.
Fleischmann, R., Adams, M., White, O., Clayton, R., Kirkness, E., Kerlavage, A., et al. (1995). Science, 269, 496–512.
Fraenkel-Conrat, H., & Olcott, H. (1945). J. Biol. Chem., 161, 259–268.
Greco, A., Bienvenut, W., Sanchez, J., Kindbeiter, K., Hochstrasser, D., Madjar, J., et al. (2001). Identification of ribosome-associated viral and cellular basic proteins during the course of infection with herpes simplex virus type 1. Proteomics, 1(4), 545–549.
Gygi, S., Rist, B., Gerber, S., Turecek, F., Gelb, M., & Aebersold, R. (1999). quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol., 17, 994–999.
Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., & Watanabe, C. (1993). Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proceedings of the National Academy of Sciences of the United States of America, 90(11), 5011–5015.
Hunt, D., Yates, J., Shabanowitz, J., Winston, S., & Hauer, C. (1986). Proc. Natl. Sci. USA, 83, 6233–6237.
James, P., Quadroni, M., Carafoli, E., & Gonnet, G. (1993). Protein identification by mass profile fingerprinting. Biochem Biophys Res Commun, 195(1), 58–64.
James, P., Quadroni, M., Carafoli, E., & Gonnet, G. (1994). Protein identification in DNA databases by peptide mass fingerprinting. Protein Sci., 3(8), 1347–1350.
Jensen, O. N., Vorm, O., & Mann, M. (1996). Sequence patterns produced by incomplete enzymatic digestion or one-step Edman degradation of peptide mixtures as probes for protein database searches. Electrophoresis, 17(5), 938–944.
Katta, V., & Chait, B. (1993). J. Am. Chem. Soc., 115, 6317–6321.
Kaufmann, R., Spengler, B., & Lutzenkirchen, F. (1993). Mass spectrometric sequencing of linear peptides by product-ion anaylsis in a reflectron time-of-flight mass spectrometer using matric-assisted laser desorption/ionisation. Rapid Commun. Mass Spectrom., 7, 902–910.
Kraus, M., Janck, K., Bienert, M., & Krause, E. (2000). Characterisation of intermolecular ?-sheet peptides by mass spectrometry and hydrogen isotope exchange. Rapid Commun. Mass Spectrom., 14, 1094–1104.
Laemmli, U. K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227(259), 680–685.
Lahn, H. W., & Langen, H. (2000). Mass spectrometry: a tool for the identifiaction of proteins separated by gels. Electrophoresis, 21, 2105–2114.
Mann, M., Höjrup, P., & Roepstorff, P. (1993). Biol. Mass Spectrum, 22, 338.
McMurry, J. (1988). Organic chemistry (2nd ed.). Belmont, CA,: Brooks/Cole Publishing Company.
Ng, W., Kennedy, S., Mahairas, G., Berquist, B., Pan, M., Shukla, H., et al. (2000). Proc. Natl. Acad. Sci. USA, 97, 12176–12181.
Nutkins, J., & Williams, D. (1989). Eur. J. Biochem.
Ohguro, H., Palczewski, K., Walsh, K., & Johnson, R. (1994). Prot Scien, 3, 2428–2434.
Pappin, D., Hojrup, P., & Bleasby, A. (1993). Rapid identification of proteins by petide mass fingerprint. Curr. Biol., 3(6), 327–332.
Patterson, S., Thomas, D., & Bradshaw, R. (1996). Application of combined mass spectrometry and partial amino acid sequence to the identification of gel separated proteins. Electrophoresis, 17, 877–891.
Rosa, J., & Richards, J. (1979). J. Mol. Biol., 133, 399–.
Sepetov, N. F., Issakova, O. L., Lebl, M., Swiderek, K., Stahl, D. C., & Lee, T. D. (1993). The use of hydrogen-deuterium exchange to facilitate peptide sequencing by electrospry tandem mass spectrometry. Rapid Commun. Mass Spectrom., 7, 58–62.
Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F., Wilm, M., Vorm, O., et al. (1996). Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci U.S.A., 93(25), 14440–14445.
Spengler, B., Lutzenkirchen, F., & Kaufmann, R. (1993). On-target deuteration for peptide sequencing by laser mass spectrometry. Org. Mass Spectrom., 28, 1482–1490.
The Arabidopsis Initiative. (2000). Nature, 408, 796–815.
The C elegans Sequencing Consortium. (1998). Science, 282, 2012–2018.
Vestal, M. L., Juhasz, P., & Martin, S. A. (1995). Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom., 9, 1044–1050.
Wang, F., & Tang, X. (1996). Biochemistry, 35, 4069–4078.
Wheeler, D., Church, D., Lash, A., Leipe, D., Madden, T., Pontius, J., et al. (2001). Database resources of the national center for biotechnology information. Nucleic acids research, 29, 11.juin.
Whittal, R., & Li, L. (1995). Anal. Chem., 67, 1950–1954.
Wilcox, P. (1967). Esterification. Meth. Enzym., 11, 605–616.
Yates, J. R., III, Speicher, S., Griffin, P. R., & Hunkapiller, T. (1993). Peptide mass maps: A highly informative approach to protein identification. Anal Biochem, 214, 397–408.
Zhang, W., & Chait, B. (2000). Anal. Chem., 72, 2482–2489.
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer
About this chapter
Cite this chapter
Bienvenut, W. et al. (2005). Improvements in the Peptide Mass Fingerprint Protein Identification. In: Bienvenut, W.V. (eds) Acceleration and Improvement of Protein Identification by Mass Spectrometry. Springer, Dordrecht. https://doi.org/10.1007/1-4020-3319-2_6
Download citation
DOI: https://doi.org/10.1007/1-4020-3319-2_6
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-3318-6
Online ISBN: 978-1-4020-3319-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)