The Peptide Spectrum page displays an image of the MS2 spectrum of the fragmented peptide.

The putative peptide sequence appears at the top of the page. Immediately below the peptide sequence are the Scan number, the Charge state, the RawScore, the DiffScore, the ZScore, the IonPercent, the Mass, the DeltaMass, the PeptideProphet score, the number of protein hits, the name of the protein sequence match, and the file name of the spectrum file within the tar.gz file. For more information on these data fields, see details on peptide columns.

Click the Blast button to the right to search the Blast protein databases for this peptide sequence.

Click the Prev button to view the previous scan in the filtered/sorted results. Click the Next button to view the next scan in the filtered/sorted results. Click Show Run to return to the details page for the run.

Finding Related MS1 Features or Other Peptide Identifications

You can click on the Find Features button to search for MS1 runs that identified features that were linked to the same peptide sequence. It will also present a list of all the peptide identifications with the same sequence in other MS2 runs from the same folder, or the same folder and its subfolders.

Ion Fragment Table

The table on the right side of the screen displays the expected mass values of the b and y ion fragments (for each of the possible charge states, +1, +2, and +3) for the putative peptide. The highlighted values are those that matched fragments observed in the spectrum.

Zooming in on a Spectrum

You can zoom in on a spectrum using the "X start" and "X end" text boxes. Change the values to view a smaller mz range.

Quantitation Elution Profiles

If your search protocol included labeled quantitation analysis using XPRESS or Q3 and you are viewing a peptide which had both light and heavy identifications, you will see three elution graphs. The light and heavy elution profiles will have their own graphs, and there will also be a third graph that shows the two overlaid. You can click to view the profiles for different charge states.

CMT and DTA Files

For COMET runs loaded via the analysis pipeline, you will see Show CMT and Show DTA buttons. For SEQUEST runs, you will see Show OUT and Show DTA buttons. The CMT and OUT files contain a list of other possible peptides for this spectrum; these are not uploaded in the database. The DTA files contain the spectrum for each scan; these are loaded and displayed, but intensities are not displayed in the Viewer. If you click the Show CMT, Show OUT, or Show DTA button, the MS2 module will retrieve these files from the file server and display them in your browser.

Note: These buttons will not appear for X!Tandem search results since those files are not associated with X!Tandem results.

Discussion

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