To support the development of robust and reproducible assays, Panorama users can now view a built in report summarizing analysis of aliquots of the same sample multiple times a day over multiple days. The MxN Reproducibility Report visualizes the reproducibility of the assay and which peptides perform best.

When a Skyline document contains multiple replicates for a protein, you can view this report from the protein details.

The report contains:

  • Protein Overview: This section is taken from the existing Passport reporting. It shows some basic metadata about the protein and its sequence (if available from the Skyline document).
  • Precursor Listing: This section shows both precursors and peptides. You can filter by the sequence length, though this doesn’t impact the rest of the reporting. You can also highlight features of the sequence as pulled from Uniprot.
    • The Sort by options let the user sort the precursors on the plots shown by:
      • Intensity
      • Sequence Location
      • Coefficient of Variation

Scrolling lower on the page, you'll see:

  • Peak Area Plot: Shows each precursor being analyzed, abbreviated by the first three amino acids of its sequence and its charge state and m/z value. It will show each replicate’s peak area, divided by run within the day, and day. A box plot will show the full range of all values. Data points will be arranged from left to right within each precursor based on their acquisition time.
  • Coefficient of Variation Plot: Shows the CV of the averages for intra-day and inter-day peak areas. It also shows the "Total CV", which is the square root of the sum of the squares of the intra and inter-day CVs.
  • Summary Table: Showing each precursor's full sequence, charge state, m/z, the three CV values, and the min, max, and mean intensities across all of the replicates.
  • Chromatograms: Clicking on a precursor in the plots or summary table will select that precursor and show its chromatograms at the bottom of the page.
    • One chromatogram per replicate is rendered, with consistent x- and y-axis scales.
    • Users can click to download a PDF or PNG of the chromatogram.

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