In the Chromatogram pane, you can view a variety of chromatograms for your data. By default, the application displays the base peak chromatogram (BPC) plot at the top and the selected ion chromatogram (SIC) plot at the bottom of the pane.
You can change which chromatograms are displayed for which raw data files; see Display multiple chromatogram plot types for a single raw data file and Display a single chromatogram plot type for multiple raw data files.
You can display the following chromatogram plot types:
- Base Peak Chromatogram (BPC)
- The BPC shows only the most intense peak in each MS spectrum at every point in the analysis.
- Because of this, the BPC for a given raw data file typically has a cleaner, simpler look than the total ion chromatogram (TIC). This is especially true for smaller molecules where all of the signal exists in a single charge state.
- The BPC also displays the absolute MS signal threshold (red line) that you set as a component detection parameter in the processing method assigned to the experiment.
- Selected Ion Chromatogram (SIC)
- The SIC shows the intensity of the signal observed at a chosen m/z as a function of retention time.
- The SIC is also known as the extracted ion chromatogram (XIC).
- Total Ion Chromatogram (TIC)
- The TIC show the sum of all the separate ion currents carried by the ions, which includes noise and background signals.
- Because of this, the TIC for a given raw data file typically appears messier or more complicated than the BPC.
- For intact oligonucleotide spectra, the TIC often looks simpler because it adds together multiple charge states.
In the chromatogram plots, the x axis represents the retention time range and the y axis indicates the relative intensity.
The green shaded area on these chromatograms (if visible) indicates the identified component peaks.
By default, the chromatographic peaks are labeled with their individual retention times, but you can change the type of label if needed. See Chromatogram pane commands.