In the Chromatogram pane, you can view the chromatograms for your data. The type of chromatogram(s) shown depends on the deconvolution method and type of MS data deconvolved as well as the Chromatogram Trace Type parameter specified in the processing method.
These chromatogram plot types include:
- Extracted Ion Chromatogram (XIC): Appears when the Calculate XIC checkbox is selected in the processing parameters (for 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. Appears when TIC is selected as the Chromatogram Trace Type in the processing parameters.
- 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. Appears when BPC is selected as the Chromatogram Trace Type in the processing parameters.
- 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.