View the predicted and experimental MS/MS spectra - BioPharma Finder Software - View the predicted and experimental MS/MS spectra - BioPharma Finder Software - BioPharma Finder Software

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 oligonucleotide analysis experiment, including the predicted and experimental MS/MS spectra.
2. On the left side of the Process and Review page, select the MS2 Spectra tab.
3. Do any of the following:
1. Select the row of a component in the Results table.
2. The spectral plots in the MS2 Spectra pane show the information stored in the reference raw data file.
3. By default, the application considers the first raw data file in an experiment as the reference raw data file.
1. For an experiment with multiple raw data files, expand (+/− icon) a component row in the Results table and select the row for a single raw data file.
2. The spectral plots in the MS2 Spectra pane show the information stored in the selected raw data file.
1. Select a scan (specific retention time (RT) point) on the base peak chromatogram (BPC) in the Chromatogram pane.
2. The spectral plots in the MS Spectra pane show the information from the selected scan.
4. On the right side of the Process and Review page, at the top of the MS2 Spectra pane, select which combination of fragmentation and resolution types that you want to view in a spectral plot from these lists.
5. The experimental data from an oligonucleotide analysis experiment might contain multiple types of MS data, including various fragmentation (CID, HCD, and either ETD or ECD) and resolution types (High or Low). The application automatically determines the specific types of data in the experiment from raw data files that you load for the experiment. For more information on the possible fragmentation types available, see Fragmentation methods.
6. If the data contains multiple data types, the application displays a separate spectral plot for every combination of fragmentation type and resolution type in the MS2 Spectra pane.

7. 

8. Each plot displays the predicted MS/MS spectrum stacked above the experimental spectrum for a particular combination (if it is available) for the selected component.
9. In both the predicted and experimental spectra, the x axis represents the mass-to- charge ratio (m/z) and the y axis indicates the relative abundance.
10. Both plots label the centroid peaks with their individual mass or m/z values, with four decimal digits for high-resolution data and two decimal digits for low-resolution data.
11. Peak labels appear in color for the identified peaks and also show their fragment ion assignments and charge states, for example, "y₉", "b₃", or "M₂₊" (doubly charged precursor ion). For more information on the fragment ions displayed, see Fragment ion types and colors.
12. For more information on the commands available in the MS2 Spectra pane, see MS2 Spectra pane commands.

13. NOTE

    You can also generate the predicted MS/MS spectrum by performing the Kinetic MS/MS model prediction.

    For more information about using the Kinetic MS/MS model prediction, see Predict MS2 spectra using the kinetic model.

5. In addition to viewing the predicted versus experimental MS/MS spectrum for a selected component, you can compare the experimental MS/MS spectra of two different components. See Compare experimental MS/MS spectra.