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.

Tutorial Requirements

  • You will need administrative permissions to complete this tutorial.
  • Your server must have the MS2 module installed. To check if the MS2 module is installed, go to > Site > Admin Console. Click Module Information. In the list of installed modules, confirm that the MS2 module is present.
  • The MS2 module is currently not available with LabKey trial servers, but it is available on a virtural machine trial instance.
  • If you are building the server from source code, you must build the MS2 module (which is included by default) and you must additionally 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.

Upload the MS2 Sample Files

In this step you will upload the sample files you just downloaded (ProteomicsDemo) to the server's file repository.

  • Navigate to the Proteomics Tutorial folder.
  • Select > Go To Module > FileContent.
  • Drag and drop the contents of the folder ProteomicsDemo into the file repository window. Note, do not import the parent directory ProteomicsDemo, as the server expects these sample files to be directly in the root of the file repository. After import, the file repository should look like the following:

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