Plots on the Component Detection page - BioPharma Finder Software - Plots on the Component Detection page - BioPharma Finder Software - BioPharma Finder Software

The following figure shows the three plots on the right side of the Component Detection page for top down analysis.

1. Chromatogram: Displays the chromatogram for each loaded raw data file.
2. By default, the Chromatogram pane displays the total ion chromatogram (TIC) for the MS data. You can view the base peak chromatogram (BPC) by right-clicking in the Chromatogram pane and choosing Chromatogram Trace Type > BPC.
3. The Chromatogram plot displays colored boxes to indicate the selected retention time (RT) ranges for several peaks. The shaded box indicates the currently selected peak.
4. To select a peak, enter the appropriate RT Range in the Peak Selection area. Alternatively, select a single scan (single RT time point) or a range of averaged scans (RT range) directly on the chromatogram.
5. See Basic chromatogram functions.
6. The chromatogram mode determines the function to apply when you drag the cursor over a retention time (RT) area of the Chromatogram pane. Select the chromatogram mode in the upper right corner of the Chromatogram pane:
7. •Averaging: Averages the spectra for all the scans in the retention time range that you drag the cursor over (left to right) and displays them in the Source Spectrum panes.
8. •Auto Zooming: Enlarges the area (intensity and time) that you drag the cursor over without changing the view displayed in the Source Spectrum panes.
9. The header in the Chromatogram pane displays the following information:
10. •Chromatogram type (TIC or BPC)
11. •Raw data file name (SLite-IxR_IdeS-red_BB1-S10-ETD25_92)
12. •The intensity (normalization level, NL) of the most abundant peak in the entire LC/MS run (3.01E9)
2. Peak # − Intact Fragmentation Source Spectrum (top pane): Displays the MS2 source spectrum for the currently selected (shaded) peak in the Chromatogram.
3. Peak # − Intact Deconvolution Source Spectrum (bottom pane): Displays the full-scan source spectrum for the currently selected (shaded) peak in the Chromatogram.
4. You must select the Intact Deconvolution checkbox in the Peak Selection area to activate the Peak # − Intact Deconvolution Source Spectrum plot.
5. A tab appears at the bottom of these panes for each raw data file loaded into the experiment. The application displays a maximum of ten raw data file tabs. Select a tab to see the chromatogram and source spectra for a particular file. To view more tabs, scroll to the right as needed.
6. See Basic spectrum functions.
7. The headers for both of the source spectra display the following information:
8. •Raw data file name (SLite-IxR_IdeS-red_BB1-S10-ETD25_92)
9. •Scan number range (#210-248)
10. •Retention time (RT) range (RT:6.464-7.4730)
11. •Number of spectra averaged to create the source spectra (AV:20)
12. •Scan filter (if any) used during the LC/MS run (F:FTMS + p ESI Full ms2 960.0000@etd25.00[350.0000–2000.0000])
13. The source spectra also appear on the Process and Review page.
14. Zooming or scaling in the source spectra does not change the m/z range that the deconvolution algorithm uses.

For each peak selected on the left side of the Component Detection page, change the source spectra by editing the RT Range parameter in the Peak Selection area at the left side of the page or by doing one of the following in the Chromatogram pane:

• (For a single scan) Use the red crosshair cursor to select a single scan on the chromatogram.
• The source spectra panes display the associated single-scan mass spectra at that time point.
• (For multiple scans) Select a region of the chromatogram to display the averaged spectrum for all the scans within that region.
• To select a region, select the Averaging option in the Mode area and then rag the red crosshair cursor across the area of interest.
• The application calculates the average spectra for the selected interval and displays them in both source spectra panes.