Now that you've configured your sample files, we can load them into the search pipeline using any of the following analysis systems:
  • X! Tandem
  • SEQUEST
  • Mascot
  • Comet

Run an X! Tandem Search

  • Click the MS2 Dashboard tab.
  • In the Data Pipeline panel, click Process and Import Data.
  • The Files panel appears and already contains the files that you downloaded in the previous step, now viewed through the file management system.
  • 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
  • Click Search to launch the X! Tandem search.
  • You will be returned to the MS2 Dashboard.

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, 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 cluster 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 MS2 runs.

Previous Step | Next Step

Discussion

previousnext
 
expand all collapse all