Installation and Use of LabKey Server for Proteomics
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
LabKey Server (formerly CPAS, the Computational Proteomics Analysis System) provides a Web?based platform for mining data from liquid chromatography?tandem mass spectrometry (LC?MS/MS) proteomic experiments. This open source platform supports systematic proteomic analyses and secure data management, integration, and sharing. LabKey Server incorporates several tools currently used in proteomic analysis, including the X! Tandem search engine, the ProteoWizard toolkit, and the PeptideProphet and ProteinProphet data mining tools. These tools and others are integrated into LabKey Server, which provides an extensible architecture for developing high?throughput biological applications. The LabKey Server analysis pipeline acts on data in standardized file formats, so that researchers may use LabKey Server with other search engines, including Mascot or SEQUEST, that follow a standardized format for reporting search engine results. Supported builds of LabKey Server are freely available at http://www.labkey.com/. Documentation and source code are available under the Apache License 2.0 at http://www.labkey.org. Curr. Protoc. Bioinform. 36:13.5.1?13.5.25. © 2011 by John Wiley & Sons, Inc.
Keywords: liquid chromatography; mass spectrometry; proteomics; data analysis; protein identification
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Protocol 1: Search Tandem Mass Spectrometry Data
- Basic Protocol 2: Viewing and Analyzing MS/MS Data in LabKey Server
- Support Protocol 1: Install and Configure LabKey Server
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
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Figure 13.5.1 The LabKey Server welcome page. View Image -
Figure 13.5.2 Screen for creating a new folder in LabKey Server. View Image -
Figure 13.5.3 Screen showing the portal page of the new folder, the MS2 Dashboard. View Image -
Figure 13.5.4 Screen for uploading files. View Image -
Figure 13.5.5 Load protein annotations. View Image -
Figure 13.5.6 Screen for monitoring the loading of protein annotations. View Image -
Figure 13.5.7 Select the mzXML data files to search for peptides. View Image -
Figure 13.5.8 Specify a search protocol. View Image -
Figure 13.5.9 View of uploaded runs on the MS2 Dashboard. View Image -
Figure 13.5.10 View of run details in the MS2 Viewer. View Image -
Figure 13.5.11 Specify how to view peptide and protein data. View Image -
Figure 13.5.12 View of peptide results by PeptideProphet score. View Image -
Figure 13.5.13 Screen for customizing view of peptide results. View Image -
Figure 13.5.14 View of spectrum information for an individual peptide. View Image -
Figure 13.5.15 View of quantitation information for an individual peptide. View Image -
Figure 13.5.16 View of ProteinProphet results. View Image -
Figure 13.5.17 View of peptides by protein assignments. View Image -
Figure 13.5.18 View of protein sequence information. View Image -
Figure 13.5.19 View of protein sequence coverage information. View Image -
Figure 13.5.20 View of protein annotations. View Image -
Figure 13.5.21 A comparison of proteins from multiple runs. View Image -
Figure 13.5.22 Screen for customizing your view of proteins from multiple runs and adding a column. View Image -
Figure 13.5.23 A comparison of proteins from multiple runs with an added column, Unique. View Image -
Figure 13.5.24 A Venn diagram of runs compared with ProteinProphet. View Image -
Figure 13.5.25 View of sensitivity and error rate information for the PeptideProphet analysis. View Image -
Figure 13.5.26 View of graphs showing distribution of PeptideProphet scores. View Image -
Figure 13.5.27 View of job status and error information for the data pipeline. View Image -
Figure 13.5.28 Example parameters for an ICAT analysis. View Image -
Figure 13.5.29 Example parameters for a SILAC analysis. View Image -
Figure 13.5.30 Example of an experimental run graph. View Image -
Figure 13.5.31 Example of an experimental run graph details view. View Image
Videos
Literature Cited
| Craig, R. and Beavis, R.C. 2004. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20:1466‐1467. | |
| Eng, J. K., McCormack, A.L., and Yates, J.R. 3rd. 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. | |
| Han, D.K., Eng, J., Zhou, H., and Aebersold, R. 2001. Quantitative profiling of differentiation‐induced microsomal proteins using isotope‐coded affinity tags and mass spectrometry. Nat. Biotechnol. 19:946‐951. | |
| Keller, A., Nesvizhskii, A.I., Kolker, E., and Aebersold, R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74:5383‐5392. | |
| Keller, A., Eng, J., Zhang, N., Li, X.J., and Aebersold, R. 2005. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1:2005.0017. | |
| MacLean, B., Eng, J.K., Beavis, R.C., and McIntosh, M. 2006. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 22:2830‐2832. | |
| Nelson, E.K., Piehler, B., Eckels, J., Rauch, A., Bellew, M., Hussey, P., Ramsay, S., Nathe, C., Lum, K., Krouse, K., Stearns, D., Connolly, B., Skillman, T., and Igra, M. 2011. LabKey server: An open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics 12:71. | |
| Nesvizhskii, A.I., Keller, A., Kolker, E., and Aebersold, R. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646‐4658. | |
| Perkins, D.N., Pappin, D.J., Creasy, D.M., and Cottrell, J.S. 1999. Probability‐based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 18:3551‐3567. | |
| Rauch, A., Bellew, M., Eng, J., Fitzgibbon, M., Holzman, T., Hussey, P., Igra, M., MacLean, B., Lin, C.W., Detter, A., Fang, R., Faca, V., Gafken, P., Zhang, H., Whiteaker, J., States, D., Hanash, S., Paulovich, A., and McIntosh, M. 2006. Computational Proteomics Analysis System (CPAS): An extensible, open‐source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 5:112‐121. | |
| Internet Resources | |
| https://www.labkey.org | |
| The LabKey Software Foundation site provides source code, documentation and community support forums for LabKey Server. | |
| https://www.labkey.com | |
| The LabKey Software site provides installers for LabKey Server and related components. LabKey Software develops LabKey Server. | |
| https://hosted.labkey.com | |
| LabKey Software's hosting site provides free, limited‐time accounts for trial usage of LabKey Server. | |
| http://www.systemsbiology.org/ | |
| The Institute for Systems Biology distributes a variety of proteomics tools, including XPRESS, PeptideProphet, ProteinProphet, and many mzXML conversion tools. | |
| http://www.thegpm.org/TANDEM/ | |
| Open source software for matching tandem mass spectra with peptide sequences. | |
| https://proteomics.fhcrc.org/CPAS/ | |
| The Fred Hutchinson Cancer Research Center's Computational Proteomics Laboratory (CPL) instance of LabKey Server. |
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