LabKey's MaxQuant module is not included in standard LabKey distributions. Developers can build the module from source code in the LabKey GitHub repository. If you are not a developer, please contact LabKey to inquire about support options.

MaxQuant is open source proteomics software used to analyze mass spectrometry data. LabKey Server can import, analyze, and present this analysis data via the MaxQuant module.

Set Up

  1. Obtain the "MaxQuant" module and install it as part of your LabKey Server distribution.
  2. Create a workspace (you must have admin permissions to complete this step):

Import MaxQuant Data

The MaxQuant software outputs a file named "summary.txt". This file can be directly imported into LabKey as follows. You must have "Author" or higher permission to complete this step.

  • Navigate to the MaxQuant Workspace folder.
  • In the Data Pipeline web part, click Process and Import Data.
  • Drag and drop the package containing the "summary.txt" file into the main panel to initiate the upload.
  • Select summary.txt and click Import Data.
  • Choose Import MaxQuant Results and click Import in the pop-up.

View MaxQuant Results

  • Return to your folder by clicking the MaxQuant Workspace link (your folder name will be shown) near the top of the page.
  • In the Experiment Runs (Imported MaxQuant Results) web part, click the "Experiment Group" number, shown here as "1".
  • The Experiment Run Details panel shows creation, location, and summary information about the experiment group.
  • Click the number of Protein Groups or Peptides to toggle the grid of data presented below.

  • Hover over the first column of any row to reveal the (Details) link.
  • Click for details about the protein group (or peptide).

Protein Search

To search for a specific protein:

  • Return to your folder by clicking the MaxQuant Workspace link.
  • In the MaxQuant Protein Search web part:
    • Enter the Protein Label value to search for within the following fields of the Protein Group table: Protein ID, Majority Protein ID, Protein Name, and Gene Name. You can enter a comma separated list for multiple value search.
    • Choose whether to search in subfolders.
    • Choose whether to limit results to exact matches.
  • Click Search.
  • The Protein Search Results page offers further search options to filter or refine the grids of results shown below.
    • Minimum probability
    • Maximum error rate
    • Restrict proteins
    • Peptide criteria

Tandem Mass Tag (TMT) Data

Tandem Mass Tag (TMT), is a way of "labeling" samples with specific chemical reagents of a known mass, allowing them to be distinguished in the mass spec data, and thus making the relative abundance of a particular protein or peptide known between samples. TMT quantitation data is automatically imported when present in the MaxQuant data.

To see TMT results, click the (Details) link for the Protein Group of interest (hover over the first column to see the link).

MaxQuant has TMT results in the following files, where X is the index of the “tag”, starting with 0:

  • peptides.txt
    • Reporter intensity corrected X
    • Reporter intensity X
    • Reporter intensity count X
    • Reporter intensity corrected X <experiment name(s)>
    • Reporter intensity X <experiment name(s)>
    • Reporter intensity count X <experiment name(s)>
  • evidence.txt
    • Reporter intensity corrected X
    • Reporter intensity X
    • Reporter intensity count X
  • modificationSpecificPeptides.txt
    • Reporter intensity corrected X
    • Reporter intensity X
    • Reporter intensity count X
    • Reporter intensity corrected X <experiment name(s)>
    • Reporter intensity X <experiment name(s)>
    • Reporter intensity count X <experiment name(s)>
  • proteinGroups.txt
    • Reporter intensity corrected X
    • Reporter intensity X
    • Reporter intensity count X
    • Reporter intensity corrected X <experiment name(s)>
    • Reporter intensity X <experiment name(s)>
    • Reporter intensity count X <experiment name(s)>
These results are imported into database tables and can be viewed through the schema browser. For example:

  • Select (Admin) > Developer Tools > Schema Browser.
  • Open the mq schema.
  • Click EvidenceTMT (under "built in queries").
  • Click View Data to see the TMT values listed above.

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