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 two plots on the right side of the Component Detection page for intact mass analysis: Chromatogram and Source Spectrum.

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 spectrum for a particular file. To view more tabs, scroll to the right as needed.

For more information on the commands available in the Chromatogram and Source Spectrum plots on th Component Detection page, see Component detection page commands.

If you select the Auto Peak Detection option as the source spectra (deconvolution) method, the application uses the Parameterless Peak Detection (PPD) algorithm as the internal peak selection mechanism to automatically select chromatographic peaks. It displays these detected peaks in blue.

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.
3. See Basic chromatogram functions.
4. The chromatogram mode determines the function to apply when you drag the cursor over a retention time area of the Chromatogram pane. Select the chromatogram mode in the upper right corner of the Chromatogram pane:
5. •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 pane.
6. •Auto Zooming: Enlarges the area (intensity and time) that you drag the cursor over without changing the view displayed in the Source Spectrum pane.
7. The header in the Chromatogram pane displays the following information:
8. •Raw data file name (Myoglobin_30pmol_microm_protein_microtrap_11min_OT_60K_1.)
9. •The intensity (normalization level, NL) of the most abundant peak in the entire LC/MS run (1.26E7)
2. Source Spectrum: Displays the source spectrum for each loaded raw data file.
3. See Basic spectrum functions.
4. The header for the source spectrum displays the following information:
5. •Raw data file name (Myoglobin_30pmol_microm_protein_microtrap_11min_OT_60K_1)
6. •Scan number range (#149-187)
7. •Retention time (RT) range (RT:3.30–4.08)
8. •(For single scans only) The intensity (normalization level, NL) of the most abundant peak in the entire LC/MS run
9. •(More multiple scans only) Number of spectra averaged to create the source spectra (AV:39)
10. •Scan filter (if any) used during the LC/MS run (FTMS + p ESI Full ms [300.00–2000.00])
11. The source spectrum also appears on the Process and Review page.
12. Zooming or scaling in the source spectrum does not change the m/z range that the deconvolution algorithm uses.

(For the Average Over Selected Retention Time source spectra (deconvolution) method) You must create a source spectrum by editing the RT Range parameter 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 pane displays 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 drag the red crosshair cursor across the area of interest.
• The application calculates the average spectrum for the selected interval and displays them in the source spectra pane.