Christie Hunter


Visualizing SWATH acquisition results in CloudConnect

CloudConnect in PeakView software 2.2 enables both the upload of data files to the OneOmics suite as well as the download of SWATH acquisition results files for viewing. This post will describe how to download and visualize the results from Extractor processing, so that you can view your raw XIC data for the quantified proteins or metabolites.

  1. To begin downloading and visualizing your results, first log in to CloudConnect. Once logged in, select Download > Load Session
  2. A Download from SCIEX Cloud dialog appears, showing your data folders contained in Data Store. Select the file of interest for download, either a *.wiff.qresult file to view your Extractor XIC peak areas or a * to view the retention time calibration data from your Extractor processing. Next, click Download.
  3. After selecting a file and beginning the download, a message will appear prompting you to navigate to the original *.wiff file on your workstation (this must be available on the local computer to visualize the raw data). Locate the requested *.wiff file and open it. A progress bar will immediately appear, showing the loading of your .qresult file.
  4. Once your *.qresult file has loaded, you will be able to review XIC peak areas for your quantified analytes of interest.
  5. An example results pane is shown below, that includes a list of proteins and their associated peptides. Select a protein to view its corresponding peptides. To view peptide XIC areas, scroll through and select a peptide of interest. XICs will appear in a window in the upper right corner. Additionally, a window showing the TIC for the particular .wiff file can be viewed by selecting it from the Quantitation > View Settings menu. Other visualization options are found there as well.
  6. Note that the proteomics results for * will look similar to the dialog shown above, except that only the retention time calibration data will be listed. You can check the quality of the retention time calibration from the Extractor processing by clicking Edit RT.
  7. The workflow is the same for visualizing your metabolomics data, with a very similar user interface. Note that there is currently no retention time calibration option used in the metabolomics SWATH Acquisition workflow.




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