View menu - Proteome Discoverer Software - View menu - Proteome Discoverer Software - Proteome Discoverer Software

View > Start Page

Opens the Start Page.

View > Layout Selector

Opens the Layout Selector so that you can select the layout to apply to the result file). For information about the Layout Selector, see Create and apply layouts.

View > Custom Tags Editor

Opens the Custom Tags Editor

CTRL+SHIFT+C

View > Display Filter

Opens the Display Filter pane so that you can set filters to refine the data. For more information, see Filtering results data.

View > Distribution Charts

Opens the Report Item Distribution chart, which displays different aspects of the search results plotted in relation to each other in scatter plots, Venn diagrams, pie charts, histograms, and bar charts. For more information, see Using the Report Item Distribution Charts.

CTRL+SHIFT+D

View > Pathway Map

Opens the pathway map view, which displays maps of the chemical pathways identified by the Wiki Pathways database for a protein. You must use the Protein Annotation node in the consensus workflow to generate the result file. For information, see Use Pathway Maps.

View > Enrichment Chart

Opens the Enrichment chart view, which provides a list of gene ontology terms, pathways, or protein families that are over- or underrepresented for a checked set of entries on the Proteins table.

CTRL+SHIFT+E

View > Details

Makes the Protein Identification Details command available when you select a protein row or makes the Peptide Spectrum Match Details command available when you select a peptide row.

CTRL+D

View > Protein Details

Opens the Protein Identification Details view, which shows how good a match is and displays information about a protein. You can also use this view to investigate biologically relevant PTMs. For information, see Use the Protein Identification Details view.

CTRL+D

View > Peptide Spectrum Match Details

Opens the Peptide Spectrum Match Identification Details view, which shows the analyzed spectra of the selected peptide sequence on the PSMs page so that you can rapidly gauge how good the match is between a sample peptide and a peptide found in the searched database. For information, see Use the Peptide Spectrum Match Identification Details view.

CTRL+D

View > Chromatogram Traces view

Opens the Chromatogram Traces view, which displays the chromatographic profiles of individual features or peaks that the application uses in calculating label-free and precursor ion quantification results. For information, see Using the Chromatogram Traces view.

View > Fragment Match Spectrum

Opens the Fragment Match Spectrum view, which shows the MS/MS spectrum used for the search, annotated with the fragments that have been assigned within a predefined mass tolerance. For information, see Using the Fragment Match Spectrum view.

CTRL+SHIFT+F

View > Precursor Isotope Pattern

Opens the Precursor Isotope Pattern view, which shows a detailed perspective of the MS scan of the precursor isotope pattern of the selected precursor. For information, see Use the Precursor Isotope Pattern view.

CTRL+SHIFT+P

View > Sequence Comparison

Opens the Sequence Comparison view, which displays the complete sequences for different proteins. You can use this view to compare similar proteins that share varying degrees of identical peptide sequences or to compare the complete sequences of different proteins associated with a single peptide. For more information, see Use the Sequence Comparison view.

View > Quan Ratio Distributions

Opens the Quantification Ratio Distributions chart, which displays the set of calculated relative ratios for the PSMs associated with the selected protein. For information about calculating peptide ratios, see Display Quantification Ratio Distribution charts.

View > Trend Chart

Opens the Trend chart, which displays the abundance of proteins or peptide groups across all sample groups. For information, see Display the Trend Chart.

View > Quan Channel Values

Displays a Quantification Channel Values chart with the following information:

• For reporter ion quantification—
• (If you select a PSM or a quantification spectrum) The absolute intensity or the signal-to-noise ratio of the reporter ions detected for the available quantification channels.
• (If you select a protein or a peptide group) The abundance of this item.
• For precursor ion quantification—
• (If you select a PSM or a quantification spectrum) The area of the isotopes detected for the available quantification channels.
• (If you select a protein or a peptide group) The abundance of this item.

For more information, see Display the Quantification Channel Values chart.

CTRL+SHIFT+N

View > Quantification Spectrum

Displays the Quantification Spectrum chart with the following information:

• For reporter ion quantification—The absolute and corrected intensities of the reporter ions.
• For precursor ion quantification—The different abundances of the identified Light, Medium, and Heavy isotopic peak patterns used to quantify a peptide.

For instructions, see Display the Quantification Spectrum chart.

CTRL+SHIFT+Q

View > Mass Recalibration View

Opens the Mass Recalibration view, which indicates how well a regression calculated a correction curve for mass recalibration. For information, see Displaying the Mass Recalibration View.

View > File Alignment View

Opens the File Alignment view, which indicates how well the retention time alignment algorithm calculate the retention time across files. For information, see Displaying the File Alignment view.

View > Summaries

Displays the Sample & Files, Analysis Settings, Validation, and Configuration summaries. For information about these summaries, see Using the Result Summaries.

View > Workflow Editor

Opens the stand-alone Workflow Editor. For information, see Working with the stand-alone Workflow Editor.