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Predicting protein post-translational modifications using meta-analysis of proteome scale data sets.

Schwartz D, Chou MF, Church GM.

Mol Cell Proteomics. 2009 Feb;8(2):365-79. doi: 10.1074/mcp.M800332-MCP200. Epub 2008 Oct 28.


Discovery of phosphorylation motif mixtures in phosphoproteomics data.

Ritz A, Shakhnarovich G, Salomon AR, Raphael BJ.

Bioinformatics. 2009 Jan 1;25(1):14-21. doi: 10.1093/bioinformatics/btn569. Epub 2008 Nov 7.


Large-scale discovery and characterization of protein regulatory motifs in eukaryotes.

Lieber DS, Elemento O, Tavazoie S.

PLoS One. 2010 Dec 29;5(12):e14444. doi: 10.1371/journal.pone.0014444.


Using the scan-x Web site to predict protein post-translational modifications.

Chou MF, Schwartz D.

Curr Protoc Bioinformatics. 2011 Dec;Chapter 13:Unit 13.16.. doi: 10.1002/0471250953.bi1316s36.


Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation.

Helsens K, Van Damme P, Degroeve S, Martens L, Arnesen T, Vandekerckhove J, Gevaert K.

J Proteome Res. 2011 Aug 5;10(8):3578-89. doi: 10.1021/pr2002325. Epub 2011 Jun 20.


Systematic analysis of protein phosphorylation networks from phosphoproteomic data.

Song C, Ye M, Liu Z, Cheng H, Jiang X, Han G, Songyang Z, Tan Y, Wang H, Ren J, Xue Y, Zou H.

Mol Cell Proteomics. 2012 Oct;11(10):1070-83. Epub 2012 Jul 13.


Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation.

Weinert BT, Schölz C, Wagner SA, Iesmantavicius V, Su D, Daniel JA, Choudhary C.

Cell Rep. 2013 Aug 29;4(4):842-51. doi: 10.1016/j.celrep.2013.07.024. Epub 2013 Aug 15.


High-throughput mass spectrometric discovery of protein post-translational modifications.

Wilkins MR, Gasteiger E, Gooley AA, Herbert BR, Molloy MP, Binz PA, Ou K, Sanchez JC, Bairoch A, Williams KL, Hochstrasser DF.

J Mol Biol. 1999 Jun 11;289(3):645-57.


VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins.

Matthiesen R, Trelle MB, Højrup P, Bunkenborg J, Jensen ON.

J Proteome Res. 2005 Nov-Dec;4(6):2338-47.


Influence of various endogenous and artefact modifications on large-scale proteomics analysis.

Bienvenut WV, Sumpton D, Lilla S, Martinez A, Meinnel T, Giglione C.

Rapid Commun Mass Spectrom. 2013 Feb 15;27(3):443-50. doi: 10.1002/rcm.6474.


Proteome-wide analysis of amino acid variations that influence protein lysine acetylation.

Suo SB, Qiu JD, Shi SP, Chen X, Huang SY, Liang RP.

J Proteome Res. 2013 Feb 1;12(2):949-58. doi: 10.1021/pr301007j. Epub 2013 Jan 18.


Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom.

Gao X, Jin C, Ren J, Yao X, Xue Y.

Genomics. 2008 Dec;92(6):457-63. doi: 10.1016/j.ygeno.2008.08.013. Epub 2008 Oct 10.


Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification.

Carroll AJ, Heazlewood JL, Ito J, Millar AH.

Mol Cell Proteomics. 2008 Feb;7(2):347-69. Epub 2007 Oct 13.


Proteome-wide prediction of acetylation substrates.

Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB.

Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13785-90. doi: 10.1073/pnas.0906801106. Epub 2009 Aug 3.


Multiple Motif Scanning to identify methyltransferases from the yeast proteome.

Petrossian TC, Clarke SG.

Mol Cell Proteomics. 2009 Jul;8(7):1516-26. doi: 10.1074/mcp.M900025-MCP200. Epub 2009 Apr 7.


ISPTM: an iterative search algorithm for systematic identification of post-translational modifications from complex proteome mixtures.

Huang X, Huang L, Peng H, Guru A, Xue W, Hong SY, Liu M, Sharma S, Fu K, Caprez AP, Swanson DR, Zhang Z, Ding SJ.

J Proteome Res. 2013 Sep 6;12(9):3831-42. doi: 10.1021/pr4003883. Epub 2013 Aug 6.


PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse.

Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M.

Nucleic Acids Res. 2012 Jan;40(Database issue):D261-70. doi: 10.1093/nar/gkr1122. Epub 2011 Dec 1.


Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response.

Bennetzen MV, Larsen DH, Bunkenborg J, Bartek J, Lukas J, Andersen JS.

Mol Cell Proteomics. 2010 Jun;9(6):1314-23. doi: 10.1074/mcp.M900616-MCP200. Epub 2010 Feb 16.


Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications.

Liu J, Erassov A, Halina P, Canete M, Nguyen DV, Chung C, Cagney G, Ignatchenko A, Fong V, Emili A.

Anal Chem. 2008 Oct 15;80(20):7846-54. doi: 10.1021/ac8009017. Epub 2008 Sep 13.


Protein structure as a means to triage proposed PTM sites.

Vandermarliere E, Martens L.

Proteomics. 2013 Mar;13(6):1028-35. doi: 10.1002/pmic.201200232. Epub 2013 Feb 4.

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