Abstract
The success of mass spectrometry based proteomics depends on efficient methods for data analysis. These methods require a detailed understanding of the information value of the data. Here, we describe how the information value can be elucidated by performing simulations using synthetic data.
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References
Eriksson J, Fenyo D. (2007) Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs. Nat Biotechnol 25, 651ā655.
Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci U S A 90, 5011ā5015.
Mann M, Wilm M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66, 4390ā4399.
Eng JK, McCormack AL, Yates JR. (1994) An approach to correlate mass spectral data with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5, 976.
Craig R, Cortens JC, Fenyo D, Beavis RC. (2006) Using annotated peptide mass Āspectrum libraries for protein identification. J Proteome Res 5, 1843ā1849.
Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7, 655ā667.
Fenyo D, Qin J, Chait BT. (1998) Protein identification using mass spectrometric information. Electrophoresis 19, 998ā1005.
Eriksson J, Fenyo D. (2004) Probity, a protein identification algorithm with accurate assignment of the statistical significance of the results. J Proteome Res 3, 32ā36.
Field HI, Fenyo D, Beavis RC. (2002) RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2, 36ā47.
Fenyo D, Beavis RC. (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 75, 768ā774.
Eriksson J, Chait BT, Fenyo D. (2000) A Āstatistical basis for testing the significance of mass spectrometric protein identification results. Anal Chem 72, 999ā1005.
Eriksson J, Fenyo D. (2004) The statistical significance of protein identification results as a function of the number of protein sequences searched. J Proteome Res 3, 979ā982.
Eriksson J, Fenyo D. (2005) Protein identification in complex mixtures. J Proteome Res 4, 387ā393.
Jensen ON, Podtelejnikov AV, Mann M. (1997) Identification of the components of simple protein mixtures by high accuracy peptide mass mapping and database searching. Anal Chem 69, 4741ā4750.
Eriksson J, Fenyo D. (2009) Peptide identification with direct computation of the significance level of the results. Proceedings of the 57th ASMS Conference on Mass Spectrometry.
Fenyo D, Ossipova E, Eriksson J. (2008) The peptide fragment mass information required to identify peptides and their post-translational modifications. Proceedings of the 56th ASMS Conference on Mass Spectrometry.
Acknowledgments
This work was supported by funding provided by the National Institutes of Health Grants CA126485, DE018385, NS050276, RR00862 and RR022220, the Carl Trygger foundation, and the Swedish research council.
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Eriksson, J., Fenyƶ, D. (2011). Modeling Mass Spectrometry-Based Protein Analysis. In: Wu, C., Chen, C. (eds) Bioinformatics for Comparative Proteomics. Methods in Molecular Biology, vol 694. Humana Press. https://doi.org/10.1007/978-1-60761-977-2_8
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DOI: https://doi.org/10.1007/978-1-60761-977-2_8
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