Using the Chromatogram Traces view - Proteome Discoverer Software - Using the Chromatogram Traces view - Proteome Discoverer Software - Proteome Discoverer Software

The Chromatogram Traces view displays the following:

• The chromatographic profiles of individual features or peaks that the application uses to calculate label-free and precursor ion quantification results
• The exact peak and feature traces that are used to derive quantification values

In addition, you can separately display the single peaks that are subsumed in feature traces to provide an even more detailed view. Closely overlapping chromatograms (or traces) in the view indicate whether peptides eluted at the same time from the column and therefore are the same peptide. They confirm the validity of the quantification results and the origin of the consensus features from the same peptide. Conversely, peaks appearing far apart in the view indicate potential false positives.

Alignment is a shift in the column during elution. It takes the pattern across different runs and shifts the retention time so that the same peptide is appropriately matched among all the runs. In peak apex alignment, the tops of the coeluting peaks have exactly the same retention time. Peak apex alignment is for cosmetic purposes only.

Abundance is the area under the curve for each trace. In the following figure, the Consensus Features page of the table associated with the selected peptide group shows the abundances displayed in the Chromatogram Traces view.

The Chromatogram Traces view can display three types of chromatograms: TIC, base peak, and Minora LC/MS peak trace. The processing workflow must include the Minora Feature Detector node to generate the latter two.

The Spectrum Selector node in the processing workflow creates the Specialized Traces page in the result file. It adds rows to the page for each input file for a base peak and TIC chromatogram. For more information on the Specialized Traces page, see The Specialized Traces page.

When the consensus workflow includes the Feature Mapper node, the Chromatogram Traces view also displays the chromatograms corrected for retention time. You can use this view to see how well the retention-time correction worked.

You can display the Chromatogram Traces view for items on the following pages of the result file. The information shown in the Chromatogram Traces view depends on the page that you select.