Abstract
Multidimensional protein identification technology (MudPIT) is an invaluable approach to identify proteins at large-scale level. Here, we describe a procedure of investigation to functional characterize the proteomic profile of complex samples such as those from cardiac tissues. In particular, we focus on the main steps concerning sample preparation, MudPIT analysis, tandem mass spectra processing, and biomarker discovery using label-free approaches. Finally, we report a data-derived systems biology approach to identify groups of proteins of over-, under-, and normal expression.
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References
Ly L, Wasinger VC (2011) Protein and peptide fractionation, enrichment and depletion: tools for the complex proteome. Proteomics 11:513–534
Nilsson T, Mann M, Aebersold R et al (2010) Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods 7:681
Horgan GW (2007) Sample size and replication in 2D gel electrophoresis studies. J Proteome Res 6:2884–2887
Yates JR, Ruse CI, Nakorchevsky A (2009) Proteomics by mass spectrometry: Approaches, advances, and applications. Annu Rev Biomed Eng 11:49–79
Braun RJ, Kinkl N, Beer M et al (2007) Two-dimensional electrophoresis of membrane proteins. Anal Bioanal Chem 389:1033–1045
Mauri PL, Scigelova M (2009) Multidimensional protein identification technology for clinical proteomic analysis. Clin Chem Lab Med 47:636–646
Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989
Comunian C, Rusconi F, De Palma A et al (2011) A comparative MudPIT analysis identifies different expression profiles in heart compartments. Proteomics 11:2320–2328
Mauri P, Deho’ G (2008) A proteomic approach to the analysis of RNA degradosome composition in Escherichia coli. Methods Enzymol 447:99–117
Park SK, Venable JD, Xu T et al (2008) A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods 5:319–322
Di Silvestre, D., Daminelli, S., Brunetti, P. et al. (2010) Bioinformatics tools for mass spectrometry-based proteomics analysis. Reviews in Pharmaceutical & Biomedical Analysis Bentham eBooks, pp. 30–51
Mauri P, Scarpa A, Nascimbeni AC et al (2005) Identification of proteins released by pancreatic cancer cells by multidimensional protein identification technology: a strategy for identification of novel cancer markers. FASEB 19:1125–1127
Regonesi ME, Del Favero M, Basilico F et al (2006) Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach. Biochimie 88:151–161
Simioniuc A, Campan M, Lionetti V et al (2011) Placental stem cells pre-treated with a hyaluronan mixed ester of butyric and retinoic acid to cure infarcted pig hearts: a multimodal study. Cardiovasc Res 90:546–556
Sokal RR, Rohlf FJ (1994) Biometry: the principles and practice of statistics in biological research, 3rd edn. Freeman, New York
Griss J, Côté RG, Gerner C et al (2011) Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data. Mol Cell Proteomics 10:M111.008490
Nesvizhskii AI, Keller A, Kolker E et al (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75:4646–4658
Zhang B, VerBerkmoes NC, Michael A et al (2006) Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics. J Proteome Res 5:2909–2918
Wang G, Wu WW, Zhang Z et al (2009) Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics. Anal Chem 81:146–159
Carvalho PC, Hewel J, Barbosa VC et al (2008) Identifying differences in protein expression levels by spectral counting and feature selection. Genet Mol Res 7:342–356
Carvalho PC, Fischer JS, Chen EI et al (2008) PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 9:316–329
Acknowledgments
This work was supported by CARIPLO Foundation (2008.2504, 2007.5312 and project - Proteomic platform, Operational Network for Biomedicine Excellence in Lombardy). The authors thank Marta G. Bitonti for MAProMA software.
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Di Silvestre, D., Brambilla, F., Mauri, P.L. (2013). Multidimensional Protein Identification Technology for Direct-Tissue Proteomics of Heart. In: Vivanco, F. (eds) Heart Proteomics. Methods in Molecular Biology, vol 1005. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-386-2_3
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DOI: https://doi.org/10.1007/978-1-62703-386-2_3
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Publisher Name: Humana Press, Totowa, NJ
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Online ISBN: 978-1-62703-386-2
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