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Proteomics by mass spectrometry: approaches, advances, and applications.
Yates JR, Ruse CI, Nakorchevsky A. Yates JR, et al. Among authors: ruse ci. Annu Rev Biomed Eng. 2009;11:49-79. doi: 10.1146/annurev-bioeng-061008-124934. Annu Rev Biomed Eng. 2009. PMID: 19400705 Review.
Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome.
Ruse CI, Tan FL, Kinter M, Bond M. Ruse CI, et al. Proteomics. 2004 May;4(5):1505-16. doi: 10.1002/pmic.200300682. Proteomics. 2004. PMID: 15188417
Quantitative dynamics of site-specific protein phosphorylation determined using liquid chromatography electrospray ionization mass spectrometry.
Ruse CI, Willard B, Jin JP, Haas T, Kinter M, Bond M. Ruse CI, et al. Anal Chem. 2002 Apr 1;74(7):1658-64. doi: 10.1021/ac0157122. Anal Chem. 2002. PMID: 12033257
Site-specific quantitation of protein nitration using liquid chromatography/tandem mass spectrometry.
Willard BB, Ruse CI, Keightley JA, Bond M, Kinter M. Willard BB, et al. Among authors: ruse ci. Anal Chem. 2003 May 15;75(10):2370-6. doi: 10.1021/ac034033j. Anal Chem. 2003. PMID: 12918979
Motif-specific sampling of phosphoproteomes.
Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd. Ruse CI, et al. J Proteome Res. 2008 May;7(5):2140-50. doi: 10.1021/pr800147u. J Proteome Res. 2008. PMID: 18452278 Free PMC article.
Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples.
Motoyama A, Venable JD, Ruse CI, Yates JR 3rd. Motoyama A, et al. Among authors: ruse ci. Anal Chem. 2006 Jul 15;78(14):5109-18. doi: 10.1021/ac060354u. Anal Chem. 2006. PMID: 16841936
Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides.
Motoyama A, Xu T, Ruse CI, Wohlschlegel JA, Yates JR 3rd. Motoyama A, et al. Among authors: ruse ci. Anal Chem. 2007 May 15;79(10):3623-34. doi: 10.1021/ac062292d. Epub 2007 Apr 6. Anal Chem. 2007. PMID: 17411013 Free PMC article.
Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search.
Lu B, Ruse CI, Yates JR 3rd. Lu B, et al. Among authors: ruse ci. J Proteome Res. 2008 Aug;7(8):3628-34. doi: 10.1021/pr8001194. Epub 2008 Jun 19. J Proteome Res. 2008. PMID: 18563924 Free PMC article.
Automatic validation of phosphopeptide identifications from tandem mass spectra.
Lu B, Ruse C, Xu T, Park SK, Yates J 3rd. Lu B, et al. Anal Chem. 2007 Feb 15;79(4):1301-10. doi: 10.1021/ac061334v. Anal Chem. 2007. PMID: 17297928 Free PMC article.
Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data.
Lu B, Motoyama A, Ruse C, Venable J, Yates JR 3rd. Lu B, et al. Anal Chem. 2008 Mar 15;80(6):2018-25. doi: 10.1021/ac701697w. Epub 2008 Feb 15. Anal Chem. 2008. PMID: 18275164 Free PMC article.
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