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Installation and Use of LabKey Server for Proteomics
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 13.5
DOI:
10.1002/0471250953.bi1305s36
Online Posting Date:
December, 2011 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
Table 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: Install and Configure LabKey Server
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
Figures
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Figure 13.5.1The LabKey Server welcome page. -
Figure 13.5.2Screen for creating a new folder in LabKey Server. -
Figure 13.5.3Screen showing the portal page of the new folder, the MS2 Dashboard. -
Figure 13.5.4Screen for uploading files. -
Figure 13.5.5Load protein annotations. -
Figure 13.5.6Screen for monitoring the loading of protein annotations. -
Figure 13.5.7Select the mzXML data files to search for peptides. -
Figure 13.5.8Specify a search protocol. -
Figure 13.5.9View of uploaded runs on the MS2 Dashboard. -
Figure 13.5.10View of run details in the MS2 Viewer. -
Figure 13.5.11Specify how to view peptide and protein data. -
Figure 13.5.12View of peptide results by PeptideProphet score. -
Figure 13.5.13Screen for customizing view of peptide results. -
Figure 13.5.14View of spectrum information for an individual peptide. -
Figure 13.5.15View of quantitation information for an individual peptide. -
Figure 13.5.16View of ProteinProphet results. -
Figure 13.5.17View of peptides by protein assignments. -
Figure 13.5.18View of protein sequence information. -
Figure 13.5.19View of protein sequence coverage information. -
Figure 13.5.20View of protein annotations. -
Figure 13.5.21A comparison of proteins from multiple runs. -
Figure 13.5.22Screen for customizing your view of proteins from multiple runs and adding a column. -
Figure 13.5.23A comparison of proteins from multiple runs with an added column, Unique. -
Figure 13.5.24A Venn diagram of runs compared with ProteinProphet. -
Figure 13.5.25View of sensitivity and error rate information for the PeptideProphet analysis. -
Figure 13.5.26View of graphs showing distribution of PeptideProphet scores. -
Figure 13.5.27View of job status and error information for the data pipeline. -
Figure 13.5.28Example parameters for an ICAT analysis. -
Figure 13.5.29Example parameters for a SILAC analysis. -
Figure 13.5.30Example of an experimental run graph. -
Figure 13.5.31Example of an experimental run graph details view.
Literature Cited
| 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. | |
Supplemental Files
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