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SearchGUI
SearchGUI Publication:
PeptideShaker: To visualize and analyze the search results we recommend the use of PeptideShaker. OMMSA Parser and X!Tandem Parser: For developer access to the search results we recommend the use of OMSSA Parser and XTandem Parser.
(Click on figure to see the full size version) NewsMay 10. 2012: SearchGUI v1.8.5 is now available:
May 6. 2012: SearchGUI v1.8.4 is now available:
April 28. 2012: SearchGUI v1.8.3 is now available:
What is SearchGUI?SearchGUI is a user-friendly, lightweight and open-source graphical user interface for configuring and running two proteomics identification search engines simultaneously, namely the Open Mass Spectrometry Search Algorithm (OMSSA) and X!Tandem. SearchGUI is based on the OMSSAGUI project. The main part of the additions have implemented by Marc Vaudel from ISAS, Germany. With help from Lennart Martens and Harald Barsnes. DownloadThe zip file in the downloads section contains the SearchGUI jar file and all the libraries needed to run the tool. In the downloads section you will also find the SearchGUI manual. Using SearchGUITo start identifying peptides and proteins using SearchGUI, download the latest version in the downloads section, unzip the downloaded file, and double-click on the SearchGUI-X.Y.Z.jar file. For additional help see the SearchGUI manual which is also found in the downloads section. In Other ToolsIt is easy to use SearchGUI in other Java tools. Below is an example of how this can be achieved: // set the parent frame of SearchGUI
JFrame parentFrame = "your parent frame";
// set the location of the configuration file to use
File configFile = new File("location of your configuration file");
// set the location of the results folder to use
File resultsFolder = new File("location of your results folder");
// create a list of the spectra files to use in the search
ArrayList<File> spectraFiles = new ArrayList<File>();
// add the spectra files to the list
spectraFiles.add(new File("spectrumFileA.mgf"));
spectraFiles.add(new File("spectrumFileB.mgf"));
// open a new SearchGUI with all parameters already filled in
SearchGUI searchGUI = new SearchGUI(
parentFrame, configFile, resultsFolder, spectraFiles);
From the Command LineThe main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. We believe that a graphical user interface would be the best choice for most users, and therefore made SearchGUI with a graphical user interface. However, it can sometimes be easier to perform a search from the command line. For example when incorporating the search into some sort of pipeline. With this in mind we have therefore included the option of using SearchGUI as a command line tool. To start SearchGUI from the command line use the following command: java -cp SearchGUI-X.Y.Z eu.isas.searchgui.SearchGUI [options and input] available options and inputs: -no_gui : hides the graphical user interface -search : starts the search automatically -omssa : enables OMSSA search -xtandem : enables XTandem search -cf config_file : the configuration file -rf results_folder : the results folder -sf spectra_file_1 [spectra_file_2] [...] : the spectra files, either as files or folders To show the usage description in the command line use the -h (or -help or -usage) option. An example command line: java -cp SearchGUI-X.Y.Z.jar eu.isas.searchgui.SearchGUI -no_gui -search -omssa -xtandem
-cf my_config_file -rf my_results_folder -sf my_spectrum_folderThis will start SearchGUI and run the search, but no GUI will be displayed. Any output from the tool or the search engines will be displayed in the command line window. Note that the automatic check for newer versions of SearchGUI will not be performed when running in command line mode. The simplest way to make your own configuration file is to select the wanted settings in the GUI version of SearchGUI and save these to a file using the "Save" option in the user interface. The command line version of SearchGUI uses the search engine locations described in the "conf/search_engines_location.oml" file. Alter the contents of this file to change the location of the search engines. User Defined ModificationsIt is straightforward to add/edit modifications via the user interface. Modifications will be available in other instances of SearchGUI and PeptideShaker for the same user/computer. Not all modifications are correctly handled by the search engines. Specifically, X!Tandem is not compatible with modifications at termini on specific amino acids. Using such a modification will result in nonsense matches which can be filtered out afterwards. This functionality is available by default in PeptideShaker. For use in other software or via command line, it is possible to add user defined modifications via an xml file. To add user-defined modifications not found in the searchGUI_mods.xml file, open the searchGUI_usermods.xml file located in the SearchGUI folder under resources/conf. Adding a modification is done by editing an XML bloc called MSModSpec: <MSModSpec>
<MSModSpec_mod>
<MSMod value="usermod1">119</MSMod>
</MSModSpec_mod>
<MSModSpec_type>
<MSModType value="modaa">0</MSModType>
</MSModSpec_type>
<MSModSpec_name>User modification 1</MSModSpec_name>
<MSModSpec_monomass>0</MSModSpec_monomass>
<MSModSpec_averagemass>0</MSModSpec_averagemass>
<MSModSpec_n15mass>0</MSModSpec_n15mass>
<MSModSpec_residues>
<MSModSpec_residues_E>X</MSModSpec_residues_E>
</MSModSpec_residues>
</MSModSpec>1. Add the corresponding “modaa” after <MSModType value="modaa"> using the following indexation (source: OMSSA): 0. modaa -- modification at particular amino acids 1. modn -- at the N terminus of a protein 2. modnaa -- at the N terminus of a protein at particular amino acids 3. modc -- at the C terminus of a protein 4. modcaa -- at the C terminus of a protein at particular amino acids 5. modnp -- at the N terminus of a peptide 6. modnpaa -- at the N terminus of a peptide at particular amino acids 7. modcp -- at the C terminus of a peptide 8. modcpaa -- at the C terminus of a peptide at particular amino acids 2. This will tell the search engines where the modification is expected to occur on the peptide. The amino-acid concerned will be specified later. 3. Replace User modification n after <MSModSpec_name> by the name of your modification. Please avoid the use of "_" in the modification names! 4. Add the modification mass after <MSModSpec_monomass>. 5. Add the amino-acid where the modification is expected to be found after <MSModSpec_residues_E>. For multiple residues, add multiple lines. We recommend having a look at searchGUI_mods.xml before modifying searchGUI_usermods.xml. Please do not change the line <MSMod value="usermod1">XYZ</MSMod>! Note that if the search results are to be opened in PeptideShaker on another computer or with another user, searchGUI_usermods.xml and peptideshaker_usermods.xml have to be identical! Result AnalysisTo visualize and analyze the SearchGUI results we recommend the use of PeptideShaker. PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines. Troubleshooting
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