For top down analysis experiments involving MS2 data, the ProSightBP Output pane on the Process and Review page displays the peak-specific results from processing the MS2 spectra in tabular format. The ProSightBP search results included the observed and theoretical monoisotopic masses, mass delta, relative abundance, charge state, and other ion information for the identified fragment ions returned by the ProSight Lite application and the Xtract deconvolution algorithm.

NOTE

Top down analysis currently supports only the Xtract deconvolution algorithm for MS2 data processing.

The ReSpect algorithm is not supported for MS2 data processing.

See Working with a top down processing method.

Procedure

  1. Open the results of your experiment from the Queue page or from the Load Results page.
  2. See Open results.
  3. The Process and Review page opens by default and displays the results of your top down analysis experiment.
  4. On the Process and Review page, select the Intact Fragmentation Results tab at the bottom left (if necessary).
  5. Select the ProSightBP Output subtab (next to the ProSightBP Fragment Map subtab) at the bottom right.
  6. Select the row of a proteoform (the level under a peak row) in the Intact Fragmentation Results table.
  7. The table in the ProSightBP Output pane displays the fragment ion and charge state results for the selected proteoform related to the top-level peak in the Intact Fragmentation Results table.
  8. The results are listed in descending order of relative abundance.
  9. See ProSightBP Output Results table parameters.
  10. image/svg+xml
    ProSightBP Output pane
  11. To view the charge state results for a proteoform, select the plus (+) sign to the left of a fragment ion row. Scroll to view more rows and columns in the table.
  12. If you load only one raw data file for the experiment or you are running a batch experiment, the results for each charge state are from one file.
  13. If you load multiple files for a multiconsensus experiment, the results for each charge state are from the combined results. To generate the combined results, the application sends the MS2 deconvolution mass results from each individual raw data file to the ProSight Lite application for searching. After receiving the individual search results, the application then combines them for display and calculates the combined sequence coverage.
  14. (For experiments containing multiple raw data files) To view the raw data file results for a proteoform, select the plus (+) sign to the left of a fragment ion row.
  15. Select the row of a raw data file (the level below a proteoform row) in the Intact Fragmentation Results table.
  16. The ProSightBP Output Results table displays the fragment ion and charge state results for the selected raw data file that is related to the higher-level proteoform and peak in the Intact Fragmentation Results table, sorted in descending order of relative abundance.
  17. You can export data from the ProSightBP Output Results table as a Microsoft™ Excel™ worksheet (.xlsx) as necessary.
  18. See Export the ProSightBP Output Results table and ProSightBP Output pane commands.