The Peptide Spectrum page displays an image of the MS2 spectrum of the fragmented peptide. This topic covers some features available from this view.

Peptide Details

The putative peptide sequence appears at the top of the Peptide Details panel. Immediately below the peptide sequence are the Scan number, Mass, Delta Mass, Charge state, etc. For more information on these data fields, see details on peptide columns.

To the left of the main spectrum image, you can select various ways to filter or expand what is shown.

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

Above the panel, use the Previous/Next links to step through the filtered/sorted results.

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 by checking the "X" and/or "Y" boxes to determine which axes dragging across the image will select. For example, if you check only X and drag, you'll select a vertical slice. If you select both X and Y, you can zoom in on a square portion of the spectrum. Click Zoom Out to return to a wider view.

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.

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