The Batch Deconvolution workflow

The Batch Deconvolution workflow is designed to perform intact protein mass determination across files using sliding window deconvolution.

The Batch Deconvolution workflow is partitioned into the Sliding Window Deconvolution and Annotate Elution Peaks workflows.

Create the Sliding Window Deconvolution

The Sliding Window Deconvolution workflow is partitioned into the Setup and All Results tabs.

Procedure

  1. From the Home screen, select the Batch Deconvolution workflow.
  2. From the Batch Deconvolution screen, select the Sliding Window Deconvolution workflow.
  3. Select Add Files in the top-right corner, then select Individual Data Files from the dropdown.
  4. Navigate to the folder containing the desired files, select them, and select Open.
  5. In the Settings tab, adjust the settings in each pane if needed.
  6. In the Identification tab, adjust the parameters to improve the identification process if needed.
  7. In the Mass Targets tab, adjust the mass and m/z tolerance for matching deconvolution results and calculating selected ion chromatograms.
  8. In the Processing Sequence tab, review the data files.
  9. Select Process Files to start the processing.
    When the processing is complete, the Mass Components, Data Files, Spectra, and Identification tabs display under the Setup and All Results tabs.
  10. In the Mass Components tab, review the results in the Mass Components table and in the Charts, Spectra, and Identification tabs.
  11. Select the Mass Components > Reporting tab to export the results as a Word or PDF report or as an Excel spreadsheet.
  12. In the Data Files tab, review the results in the Data File Summaries table and in the Charts, Spectra, and Identification tabs.
  13. Select the Data Files > Reporting tab to export the results as a Word or PDF report or as an Excel spreadsheet.
  14. In the Spectra tab, review the results for each deconvoluted spectrum.

Create the Annotate Elution Peaks

The Sliding Window Deconvolution workflow is partitioned into the Setup and All Results tabs.

Procedure

  1. From the Home screen, select the Batch Deconvolution workflow.
  2. From the Batch Deconvolution screen, select the Annotate Elution Peaks workflow.
  3. Select Add Files in the top-right corner, then select Individual Data Files from the dropdown.
  4. Navigate to the folder containing the desired files, select them, and select Open.
  5. In the Settings tab, adjust the settings in each pane if needed.
  6. In the Peaks tab, add regions of chromatogram for mass deconvolution by right-clicking on the regions of interest.
  7. In the Identification tab, adjust the parameters to improve the identification process if needed.
  8. In the Processing Sequence tab, review the data files.
  9. Select Process Files to start the processing.
    When the processing is complete, the Peaks, Mass Components, Data Files, Spectra, and Identification tabs display under the Setup and All Results tabs.
  10. In the Peaks tab, review the results in the Annotated Trace Peaks table and in the Charts, Spectra, and Identification tabs.
  11. Select the Peaks > Reporting tab to export the results as a Word or PDF report or as an Excel spreadsheet.
  12. In the Mass Components tab, review the results in the Mass Components table and in the Charts, Spectra, and Identification tabs.
  13. Select the Mass Components > Reporting tab to export the results as a Word or PDF report or as an Excel spreadsheet.
  14. In the Data Files tab, review the results in the Data File Summaries table and in the Charts, Spectra, and Identification tabs.
  15. Select the Data Files > Reporting tab to export the results as a Word or PDF report or as an Excel spreadsheet.
  16. In the Spectra tab, review the results for each deconvoluted spectrum.