Tutorial - inChorus

This video is going to address the inChorus meta protein id tool. Performing a search with the same data by different search engines is useful both for finding new proteins and confirming others. You can perform an inChorus search using PEAKS Protein ID, X!Tandem, OMSSA, Mascot and Sequest. For this example we will be performing a local search using the X!Tandem and OMSSA search engines with PEAKS.

1) Click on the orbisample.mzxml file
2) Then click the inChorus Search toolbar icon or select “inChorus Search” from the “Tools” menu.

The inChorus search window will open. Check the “PEAKS Protein ID” box and select the name.

Set the parameters to:

  • Parent ion error tolerance to 0.1 daltons using monoisotopic mass
  • Fragment mass error tolerance to 0.8 daltons
  • Enzyme to trypsin
  • Carboxymethyl as our fixed PTM
  • Oxidation M and Deamidation as variable
  • Search through the Sample DB database
Click Ok.

Check the “X!Tandem” box.

  • Select the Sample DB database
      • All species
  • Fragment mass error to 0.8
  • Carboxymethyl C as complete modification
  • Oxidation M and Deamidation N and Q as potential modifications
  • Trypsin as our cleavage site
  • FTICR as our predefined method
To save time, we are now going to run an OMSSA search, but if you have Mascot or Sequest, the configurations are pretty straight forward to launch those engines. Check the “OMSSA” box and select the name.

  • Trypsin
  • Sample DB
      • All Species
  • Carboxymethyl C as fixed
  • Deamidation N and Q and Oxidation M
  • Precursor mass to 0.1
  • Fragment mass to 0.8
  • monoisotopic
Click Ok.

When the inChorus search is complete you should see many new additions in the “Project View” panel.
Presented here are individual reports for PEAKS, X!Tandem and OMSSA as well as an inChorus report that compares the individual reports. To see each of these reports, double click on the report that you would like to see in the “Project View” panel.

The inChorus report contains most of the information that is seen in a PEAKS Protein ID results file.

Click on the “Peptide View” tab

The “Peptide View” of an inChorus report contains the scores received by each search engine involved in the inChorus search. A “–” indicates that the search engine did not find that a protein sequence for that particular spectrum. Notice that while PEAKS Protein ID found spectra 1-5, X!Tandem found 1, 5 and OMSSA found 1, 3, 4 and 5.

Click on the “Protein View” tab.

The “Protein View” of an inChorus report displays the proteins that were found and indicates by checkmarks whether the different search engines found that protein or not. In this case, the X!Tandem and OMSSA searches did not generate any extra results that PEAKS did not find but helped to confirm that the first protein is good match.

Click here to continue on to the next tutorial, dedicated to SPIDER -homology searching tool.

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