Upload a custom analysis protocol

Follow these steps on the Your Protocols to upload a custom (user-defined) analysis protocol. Supported file formats are .xml and .json.

You can upload custom analysis protocols to PAS. For a DDA-based analysis, an .xml file is required. For a DIA- or Proteogenomics-based analysis, a .json file is required.

1. On the sidebar menu, select  Analysis Protocol.

2. Select the Your Protocols tab.

3. Select Upload Potocol to open the Analysis Protocol dialog.

4. Complete the fields.

   • Name — Enter a unique name for the protocol.

   • Analysis Type — Select the MS method.

     • DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual precursor ion.

     • DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.

     • PROTEOGENOMICS — Identifies variant peptides arising from single nucleotide variants or short insertions and deletions.

   • Analysis Engine — Select an analysis engine (e.g., Max Quant). For information about the analysis engines supported by PAS, see Analysis protocols.

   • Species — The selected species for the protocol.

   • Description — Enter a description for the protocol.

   • Notes — Enter any additional information about the protocol.

5. Upload the protocol's parameter file:

   1. Select Upload to open the Upload File dialog.

   2. Drag-and-drop the file or select Browse to navigate to and select the file.

   3. Select Upload.

6. On the Analysis Protocol dialog, select Save.