The Peptide Mapping workflow

The Peptide Mapping workflow is designed for the analysis of targeted peptide mapping data for an antibody or protein of interest.

The Peptide Mapping workflow only contains the Setup tab. Other tabs display after processing the data.

Create a Peptide Mapping workflow

Procedure

  1. From the Home screen, select the Peptide Mapping workflow.
  2. In the Experimental Design tab, select Add Files, then select Individual Data Files, navigate to the folder containing the desired files, and select Open.
  3. In the Settings tab, select the method template and adjust the settings if needed.
  4. In the Search Space tab, select Import FASTA Sequence, navigate to the folder containing the desired sequence file, and select Open.
  5. In the Search Space tab, adjust the search settings, and select the desired proteases and variable and fixed modifications if needed.
  6. In the Processing Queue tab, select Process Files.
    When the processing is complete, the Peptides, Proteins, and Spectral Matches tabs display.
  7. In the Peptides tab, review the results in Charts, Spectral Matches, and Precursor Spectra.
  8. Select the Peptides > Reporting tab, then export the results as a Word or PDF report or as an Excel spreadsheet.
  9. In the Proteins tab, review the protein results.
  10. Select Export to export the results as a spreadsheet.
  11. In the Spectral Matches tab, review the spectral matches results.
  12. Select Export to export the results as a spreadsheet.