For our sample data, we will use three mzXML files from the paper 'Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane' (Marelli et al.). One of the research goals was to identify proteins associated with peroxisomes that were not previously associated.

Install the Proteomics Binaries

In order to complete this tutorial, your server must have the proteomics binaries available. If they are not already available on your server, the easiest way to complete this tutorial is to install a new local instance of LabKey Server on a Windows machine.

In the installation wizard, on the Install Proteomics Libraries page, make sure to place a checkmark next to Download proteomics analysis tools.

If you are building the server from source code, obtain the proteomics analysis tools using these instructions.

Obtain the Sample MS2 Data Files

Download the sample data files. (Choose either zip or tar format, whatever is most convenient for you.)


Create a Proteomics Folder for the Sample Data

Create a new project or folder inside of LabKey server to store the demo data.

  • Log into your server. You will need administrative permissions to complete this tutorial.
  • Navigate to your tutorial workspace.
  • Create a new folder named "Proteomics Tutorial". Choose folder type "MS2".

Set Up the Pipeline

  • In the Data Pipeline web part of the new folder, click Setup.
  • Select Set a pipeline override.
  • Enter the path to the sample files you download and extracted. (In our example: C:\ProteomicsDemo)
  • Click Save.
  • Look for the confirmation message (in green text): "The pipeline root was set to..."

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