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Chromatograms present in the Skyline file can be viewed from within Panorama with several display customization options. Users have the option to see multiple peptides or small molecules in the same chromatogram.

After loading your Skyline document into Panorama, click the name of the file to open the details page. Then click the name of a protein / label to open the Protein/Molecule List Details page.

Multiple Peptides Per Chromatogram

When the protein contains many peptides, it can be useful to see the chromatograms for several peptides in one plot.

On the protein details page, scroll down to the Chromatograms section where you will a legend showing the colors assigned to the individual peptides present. By default all peptides are included, unless you select a subset using the checkboxes. The chromatograms below all use this scheme to show the same series of peptides for each replicate.

Use the Row Size menu to control the display size of the SVG plots; options are 1, 2, 3, 4, 5, or 10 per row.

Select Peptides for Chromatograms

By default, all peptides will be included in the chromatograms, unless you use the checkboxes in the Peptides panel to select only a subset.

Display Chart Settings

Open the Display Chart Settings panel to adjust your chart.

  • Set the Chart Width and Height and opt to Synchronize the X- and/or Y-axis.
  • Use the Replicates dropdown to multi-select the specific replicates for which you want to see the chromatograms, making it easier to compare a smaller number of interest.

Click Update and you will see only the multi-peptide chromatograms for your selected replicates.

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