Using the scan‐x Web Site to Predict Protein Post‐Translational Modifications
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- Abstract
- Table of Contents
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Abstract
The recent plethora of proteomic mass spectrometry data is providing evidence that almost every protein in the cell undergoes some form of post?translational modification. We describe a protocol to use the scan?x Web site to view predicted acetylation sites in the human proteome and predicted phosphorylation sites in the human, mouse, fly, and yeast proteomes with high specificity. This tool is accessible from virtually any computer with a Web browser. The only requirement is a means of searching for a protein of interest in one of the represented organisms. Curr. Protoc. Bioinform. 36:13.16.1?13.16.8. © 2011 by John Wiley & Sons, Inc.
Keywords: acetylation; phosphorylation; post?translational modification (PTM); scan?x; motif?x; mass spectrometry; proteomics
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Protocol 1: Using the scan‐x Web Server to View Predicted Post‐Translational Modification Sites on a Protein of Interest
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
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Figure 13.16.1 scan‐x main search page. This screenshot of the scan‐x main parameters/search page shows the appropriate parameters for the mouse Rb1 example provided in the . An in‐depth description of the various parameters can be found in the main text. View Image -
Figure 13.16.2 scan‐x job submission page for the Rb1 example. This screenshot shows the job submission page users are brought to upon pressing the “Search” button. Although this page typically will auto‐refresh, on occasion it may be necessary to manually refresh this page using the “Check Again” button or the Web browser “reload” button to view the results. View Image -
Figure 13.16.3 scan‐x Web search heading and parameters for the Rb1 example. This screenshot shows the uppermost portion of the scan‐x results page for the Rb1 example described in the . View Image -
Figure 13.16.4 scan‐x prediction results for the Rb1 example. This screenshot shows the scan‐x results for the Rb1 example described in the . An in‐depth explanation of the results view is provided in the text. View Image -
Figure 13.16.5 Understanding scan‐x results text box. This screenshot shows a key for understanding scan‐x results which can be found at the bottom of every scan‐x search results page. View Image
Videos
Literature Cited
| Bodenmiller, B., Malmstrom, J., Gerrits, B., Campbell, D., Lam, H., Schmidt, A., Rinner, O., Mueller, L.N., Shannon, P.T., Pedrioli, P.G., Panse, C., Lee, H.K., Schlapbach, R., and Aebersold, R. 2007. PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol. Syst. Biol. 3:139. | |
| Gnad, F., Gunawardena, J., and Mann, M. 2011. PHOSIDA 2011: The posttranslational modification database. Nucleic Acids Res. 39:D253‐D260. | |
| Hornbeck, P.V., Chabra, I., Kornhauser, J.M., Skrzypek, E., and Zhang, B. 2004. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4:1551‐1561. | |
| Ingrell, C.R., Miller, M.L., Jensen, O.N., and Blom, N. 2007. NetPhosYeast: Prediction of protein phosphorylation sites in yeast. Bioinformatics 23:895‐897. | |
| Obenauer, J.C., Cantley, L.C., and Yaffe, M.B. 2003. Scansite 2.0: Proteome‐wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31:3635‐3641 | |
| Schwartz, D. and Gygi, S.P. 2005. An iterative statistical approach to the identification of protein phosphorylation motifs from large‐scale data sets. Nat. Biotechnol. 23:1391‐1398. | |
| Schwartz, D., Chou, M.F., and Church, G.M. 2009. Predicting protein post‐translational modifications using meta‐analysis of proteome scale data sets. Mol. Cell Proteomics 8:365‐379. | |
| Key Reference | |
| Schwartz et al., 2009. See above. | |
| Original description of the scan‐x algorithm. | |
| Internet Resources | |
| http://scan‐x.med.harvard.edu | |
| Home page for the scan‐x version 1.1 Web tool. | |
| http://phosphosite.org | |
| A large database of experimentally determined post‐translational modification sites. | |
| http://phospho.elm.eu.org | |
| A large database of experimentally determined phosphorylation sites. | |
| http://scansite.mit.edu | |
| An alternative, widely used Web tool for kinase‐specific phosphorylation prediction. |
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