Abstract
Protein identification by mass spectrometry (MS) is an important technique in proteomics. By searching an MS spectrum against a given protein database, the most matched proteins are sorted using a scoring function and the top one is often considered the correctly identified protein. Peptide mass fingerprinting (PMF) is one of the major methods for protein identification using MS technology. It is faster and cheaper than the other popular technique - Tandem Mass Spectrometry. Key bioinformatics issues in PMF analysis include designing a scoring function to quantitatively measure the degree of consistency between a PMF spectrum and a protein sequence and assessing the confidence of identified proteins. In this chapter, we will introduce several scoring functions that were developed by others and us. We will also provide a new statistic model to evaluate the confidence of the score and make an improvement for ranking proteins in protein identification. Our developments have been implemented in a software package “ProteinDecision,” which is available at http://digbio.missouri.edu/ProteinDecision/.
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References
Zhou, G., Li, H., DeCamp, D., Chen, S., Shu, H., Gong, Y., Flag, M., Gillespie, J., Hu, N., Taylor, P., Buck, M.E., Liotta, L.A., Petricoin III, E.C., and Zhao, Y. (2002) 2-D differential in-Gel electrophoresis for the identification of human esophageal squamous cell cancer specific protein markers. Molecular & Cellular Proteomics 1(2):117-124.
Wool, A. and Smilansky, Z. (2002) Precalibration of matrix-assisted laser desorption/ionization-time of flight spectra for peptide mass fingerprinting. Proteomics 2:1365-1373.
Harris, W.A., Reilly, P.T.A., and Whitten, W.B. (2005) Transportable real-time single-particle ion trap mass spectrometer. Review of Scientific Instruments 64:102-108.
Doucette, A. and Li, L. (2001) Investigation of the applicability of a sequential digestion protocol using trypsin and leucine aminopeptidase M for protein identification by matrix-assisted laser desorption/ionization - time of flight mass spectrometry. Proteomics 1:987-1000.
Pappin, D.J.C., Hojrup, P., and Bleasby, A.J. (1993) Rapid identification of proteins by peptide-mass fingerprinting Transportable. Current Biology 3:327-332.
Perkins, D.N., Pappin, D.J.C., Creasy, D.M., and Cottrell, J.S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567.
Clauser, K.R., Baker, P.R., and Burlingame, A.L. (1999) Role of accurate mass measurement (+/-10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Analytical Chemistry 71:2871-2882.
Zhang, W.Z. and Chait, B.T. (2000) ProFound: An expert system for protein identification using mass spectrometric peptide mapping information. Analytical Chemistry 72:2482-2489.
Margnin, J., Masselot, A., Menzel, C., and Colinge, J. (2004) OLAV-PMF: A novel scoring scheme for high-throughput peptide mass fingerprinting. Journal of Proteome Research 3:55-60.
Eriksson, J. and Fenyo, D. (2004) Probity: A protein identification algorithm with accurate assignment of the statistical significance of the results. Journal of Proteome Research 3:32-36.
Ganapathy, A., Wan, X., Wan, J., Thelen, J., Emerich, D.W., Stacey, G., and Xu, D. (2004) Statistical assessment for mass-spec protein identification using peptide fingerprinting approach. Proceedings of the 26th International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 3051-3054. Sept. 1-5, 2004, San Francisco, CA.
Song, Z., Chen, L., Ganapathy, A., Wan, X., Brechenmacher, L., Tao, N., Emerich, D., Stacey, G., and Xu, D. (2007) Development and assessment of scoring functions for protein identification using peptide mass fingerprinting data. Electrophoresis 28:864-870.
Song, S., Chen, L., and Xu, D. (2009) Confidence assessment for protein identification by using peptide-mass fingerprinting data. Proteomics 9:3090-3099.
Acknowledgments
This work has been supported by the MU-Monsanto Program. Zhao Song is also supported by the Shumaker Fellowship. The authors like to acknowledge the Proteomics Center at the University of Missouri-Columbia for MS services. We would like to thank Beverly DaGue, Brian Mooney, David Emerich, Gary Stacey, Jay Thelen, Chi-Ren Shyu, Guohui Lin, Chao Zhang, Yu Chen, Yang Guo, and Zhihai He for helpful discussions and/or technical assistance.
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Song, Z., Chen, L., Xu, D. (2010). Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_2
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DOI: https://doi.org/10.1007/978-1-60761-444-9_2
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