NOTE: The documents for the Enterprise Pipeline are currently in draft form. They will be periodically updated.

These instructions explain how to configure a Project to use the Enterprise Pipeline for MS1 and MS2 searches. For these instructions, we will create a new Project and configure a Pipeline for the new Project.

Before you performing the tasks below, you must:

Create a New Project to Test the Enterprise Pipeline

You can skip this step if a Project already exists that you would rather use.

  1. Log on to your LabKey Server using a Site Admin account
  2. Create a new Project with the following options
    • Project Name = PipelineTest
    • Select MS2 Folder Type radio button
  1. Choose the default settings during the Project Creation.
For more information on Creating a Project see Create a Project or Folder.

Configure the Project to use the Enterprise Pipeline

The following information will be required in order to configure this Project to use the Enterprise Pipeline

  • Pipeline Root Directory
  • Pass Phrase for User Key File
NOTE: Different User Cert/Key pairs can be used for different Pipelines.

Set Up the Pipeline

  1. Click on the Setup button in the Data Pipeline web part
  2. Enter in the following information
    • Path to the desired Pipeline Root directory on the Web Server
    • Specific settings and parameters for the relevant section
  1. Click on the Set button
  2. Goto the MS2 Dashboard, by clicking the PipelineTest link in the upper left pane

Test the Enterprise Pipeline

To test the Enterprise Pipeline, simply

  • Click on the Process and Upload Data button in the Data Pipeline web part
  • Navigate to an mzXML file with the Pipeline Root Directory and hit the X!Tandem Pepitide Search button to the right of the filename.


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