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OMSSA Browser
SUPPORT POLICY for the OMSSA Browser
Scientists at the National Center for Biotechnology Information (NCBI) develop a variety of computational tools as part of their own research and make them available to the scientific community. Descriptions of software tools and algorithms are published in appropriate journals, and both executables and source code are available upon request from the authors. However, NCBI cannot provide user support for these tools. If you have questions on the use of the Browser, first consult the on-line help as well as the original sources. As a last resort, you may send e-mail to info@ncbi.nlm.nih.gov, however, you should not expect a prompt reply.
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The OMSSA Browser is downloadable program that allows you to run OMSSA MS/MS searches and graphically view the search results. These search results can come from a search run in the browser, on our public search site, or using the command line version of OMSSA. Note: to use the browser with the output from the command line version of OMSSA, please use the "-w" option along with "-ox resultsfile.omx" or "-ob resultsfile.oms". The OMSSA browser is available for Windows and
MacOS X
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The OMSSA browser can be downloaded for Windows and Mac OS X.
After the browser is installed, protein sequence libraries need to be downloaded in order to run OMSSA search.
- Download Protein Library Files
The browser needs local protein sequence libraries to run the OMSSA search. By selecting the menu item "Tools->Download Protein Libraries" after downloading, installing, and starting the browser, the browser will display the dialog shown below for downloading the default protein library files. If you click the button 'Download', downloading of
the default (standard) protein libraries will begin. Note that after the protein libraries are downloaded, you need not repeat this step until you need a new version of the protein libraries.
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- Merging Peak List Files
OMSSA works more efficiently if multiple spectra are searched at once, up to a few thousand spectra. If you wish to perform the optional step of merging spectrum files, the OMSSA browser provides a merge file dialog. First, select the menu item "Tools->Merge/Convert Files->Merge MS Peak List File" and a dialog will appear for merging peak list files in *.dta, *.mgf or *.pkl format. Select the import file format. Select either "add files" or "add file folders" depending on whether you want to specify individual files or folders containing the files. Click on the "Add..." button to select either the files or folders to merge. Click the 'Merge' button and the browser will ask for a merged file name and then start merging.
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- Run an OMSSA Search
The browser includes the OMSSA search engine. By selecting the menu "Tools->Run OMSSA Search", a dialog is displayed for running an OMSSA search. First, select a file containing spectra using the "choose file" button. Then enter an output file name in the "output file path" control. Then select the search parameters, such as enzyme, species, fixed and variable modifications, and mass tolerances and types. To run the search, click the "run" button. When a search is done, the search result is saved to the file you specified and loaded onto the browser.
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- View Search Result
The OMSSA browser displays and processes search results at the level of protein, peptide and spectrum, producing the corresponding interactive views with user options available.
Protein Summary View: This is the default view at loading an OMSSA result. It summarizes all unique protein sequences from significant peptide hits, sorted by a Protein-Score. The Protein-Score is a protein hit ranking score derived from multinomial and likelihood ratio for bottom-up protein identification and is intended to indicate the likelihood that a particular protein is observed.
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Protein Coverage Detail View: This is a child window of Protein Summary View for a given unique protein sequence. It shows the amino acid coverage (in red) of the protein sequence(s) along with protein annotations and a digested peptide list.
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Spectrum View: For visual inspection of spectra and corresponding peptide hits. The view has user settable layouts: single or dual spectrum panels with or without a text panel that describes search parameters, matched product ions, modifications, etc. Features includes peak labeling settings, spectrum display scale adjustments (both m/z and intensity), and zoom in/zoom out via mouse press/click/move. Spectrum views can be saved to an image file in emf (for Microsoft Windows only) or png format, or copied and pasted into other applications. The text panel also can be saved to csv (excel) files or copied and pasted into other applications.
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More Views: go to Detailed On-Line Help
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