The following table describes the types of information on the Process and Review page.

Process and Review page parameters

Parameter

Description

Results table

Displays, at the upper level, the components and their peptide sequences, retention times, modifications, and detected masses, along with their confidence scores.

When the HCP search feature is enabled, it displays the Comet E-Value, Host Cell Protein, Protein Family and Other Proteins Description.

At the lower level, the table displays all of the raw data files that are loaded for the experiment and their information.

Chromatogram pane

Displays the chromatograms for the component or raw data file that you select in the Results table.

Relative Intensity (y axis)

Displays the ratio of the intensity of a specific peak to the intensity of the peak with the highest intensity.

RT (min) (x axis)

Displays the retention time (RT) of the spectrum, which is the time after injection at which a compound elutes. Retention time can also refer to the total time that the compound is retained on the chromatographic column.

Peptide Match ID Details pane

Provides detailed fragment information for a selected component when MS/MS data is available. Editable in real-time.

Trend Ratio pane

Displays the bar plots for the ratios between various conditions and the reference condition for the component selected in the Results table.

Ratio value (y axis)

Displays the Avg MS Area value for a particular condition/Avg MS Area value for the reference condition.

Ratio conditions (x axis)

Displays the names of the various conditions and the name of the reference condition.

Trend MS Area pane

Displays the bar plots for the MS Area values for the component that you select in the Results table for each raw data file used in the experiment.

MS Area value (y axis)

Displays the MS Area values from each of the individual raw data files assigned to a particular condition.

Condition−Raw data file (x axis)

Displays the names of the various conditions and their assigned raw data files used in the experiment.

Peptide Sequence Coverage pane

Displays the Fragment Coverage Map, including the peptide sequence information and the color-coded fragment ions.

Protein Sequence pane

Displays the protein sequence assigned to the experiment, highlighting the peptide sequence corresponding to the component selected in the Results table.

Full Scan Spectra pane

Displays the deconvoluted and full-scan spectra with mass and m/z information.

Relative Abundance (y axis)

Displays the ratio of the abundance of a specific peak to the abundance of the peak with the highest abundance.

Mass or m/z (x axis)

Displays the mass or mass-to-charge ratio of the ions formed from molecules.

MS2 Spectra pane

Displays the predicted spectrum stacked on top of the experimental spectrum.

Relative Abundance (y axis)

Displays the ratio of the abundance of a specific peak to the abundance of the peak with the highest abundance.

m/z (x axis)

Displays the mass-to-charge ratio of ions formed from molecules.

HCP Proteins pane

Displays HCP contaminants detected in your experiment.

Real Time Optimization pane

Displays the same parameters as those on the Parameters pages (in the processing method editing wizard), so that you can adjust these parameters and reprocess the experiment in real time.