Below are links to the documentation for each workflow, which include instructions for installing, running, and interpreting the output of each workflow.

DIA - peptide search and quantification

This workflow runs msconvert, EncyclopeDIA, and Skyline to run a DIA workflow for discovering and quantifying peptides.

See: DIA Workflow Documentation

DDA - peptide search

This workflow runs msconvert, Comet, Percolator, and Limelight to run a DDA workflow for bottom up proteomics and subsequent visualization and sharing.

See: DDA Workflow Documentation

Open Modification DDA

This workflow runs msconvert, Magnum, Percolator, and Limelight to run a DDA workflow for discovery of peptides and modification or adduct masses that may be present in the data, without a priori knowledge of what masses may be present.

See: Open Modication Workflow Documentation

AWS Batch

Any of these workflows may be optionally run using AWS Batch. Follow the link below for instructions to set up, configure, and run workflows using AWS Batch.

See: Open AWS Batch Documentation

Funding & Attribution

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.