This workflow is designed to go from RAW files to a Skyline document with search and quantification results. These results may be optionally uploaded to PanoramaWeb/ProteomeXchange. It makes use of either DIA-NN or EncyclopeDIA to perform the search.
Please use the links below to navigate to pages describing how to install and run the workflow, how to retrieve results, and how to set up AWS Batch to run the workflow in the cloud.
If you need help, have ideas for new features, encounter a problem, or have any questions or comments, please contact Michael Riffle at mriffle@uw.edu.
.. toctree:: :maxdepth: 2 self overview how_to_install how_to_run workflow_parameters results set_up_aws
This work was made possible with funding from IARPA via the TEI-REX program (Contract #: W911NF2220059). The contents of these documents are purely technical in nature, with no opinions or perspectives of the US Goverment's interests in TEI-REX.