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Now that the sample files are on the server, we can load them into the search pipeline using any of the following analysis systems:

  • X!Tandem
  • Mascot
  • Comet

Run an X!Tandem Search

  • Click the Proteomics Tutorial link to return to the main folder page.
  • In the Data Pipeline panel, click Process and Import Data.
  • Open the folder Peroxisomal_ICAT by clicking in the left panel.
  • Select the three files in the folder and click X!Tandem Peptide Search. If you don't see the link to click, try making your browser window wider.

Select the Analysis Protocol

Next, you'll choose the FASTA file against which you wish to search and configure other parameters, like quantitation. Save the information as a protocol for use with future searches.

The sample contains an Analysis Protocol which is already configured to search an ICAT MS2 run and which instructs X!Tandem to use the k-score scoring algorithm.

  • Select the Analysis Protocol named "k_Yeast_ICAT". (Note this is not the default selection; use the dropdown menu to choose it. If you don't see it, return to the upload step and make sure the .labkey directory was uploaded to your server.)
  • Click Search to launch the X!Tandem search.
  • You will be returned to the main Proteomics Tutorial page.

Check the Search Status

While the X!Tandem search is underway, the status of search jobs is shown in the Data Pipeline panel.

  • In the Data Pipeline panel, you can see the status of the searches progress.
  • Click links in the Status column to view detailed status and the pipeline log for that job.
  • Note that as the jobs are completed, the results appear in the MS2 Runs panel below.

Searching the sample files takes one or two minutes each. On a pipeline installation running in production, you can set up email notifications for completed searches, but when working through the tutorial on your local computer, just wait until the jobs are all done and then refresh the full page in the browser to see the three runs listed in the MS2 Runs web part below.

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