In the Chromatogram pane, you can view several types of chromatograms for your data.
You can change which chromatograms are displayed by right-clicking anywhere in the pane to open the shortcut menu, selecting Chromatogram Trace Type, and selecting the checkbox for the chromatogram type you want to display.
These chromatogram plot types include:
- Extracted Ion Chromatogram (XIC): Appears when the Calculate XIC checkbox is selected in the processing method (Xtract deconvolution of full-scan MS data).
- The XIC shows the intensity of the signal observed at a chosen m/z as a function of retention time.
- The XIC is also known as the selected ion chromatogram (SIC).
- Total Ion Chromatogram (TIC): Available for all experiments.
- 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 protein/oligonucleotide spectra, the TIC often looks simpler because it adds together multiple charge states.
- Base Peak Chromatogram (BPC): Available for all experiments.
- 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.
In the chromatogram plots, the x axis represents the retention time range and the y axis indicates the relative intensity.