Multiplexed Project - mgtools/MetaProD Wiki

Multiplexed projects require a few more steps to add compared to a label-free project.

This is an overview of how to add a multiplexed project.

Add a New Project


Add a new project. In this case, it is called example2. Hit SAVE (bottom right) to save the project.

Add Search Settings for the Project


In the search settings page, assign the project to the new project you added.

Configure the MS settings as desired.


At the bottom of the search settings config, add the desired mods. In this case, we are adding a TMT 10-plex project so we add TMT 10-plex of K and TMT 10-plex of peptide N-term as fixed mods (along with any other desired mods, such as Oxidation of M as a variable mod).

If the mod you desire is not added to the system, it will need to be added first.


The mod lists admin page lets one add mods, as desired. The default configuration (if ./loadconfig is used) will load TMT 6-plex, TMT 10-plex, and TMT 11-plex mods. iTRAQ is supported by the software and will be added to the default mods, in the future. The full list of supported mods is available at: (use the Name field).

Add the Reagent (if not yet added)

Reagents (TMT 10-plex, etc.) need to be added to the system. This lets the software know what the individual labels (e.g., TMT_126) so they can be assigned.


TMT 6-plex, TMT 10-plex, and TMT 11-plex are added by default. More reagents will be added by default in the future.

Configure Samples

It is important to assign the individual files to samples. The samples page lets one add samples to the system.


Each fraction group or individual file (if no fractions) should be assigned a sample.

Assign Samples

Assign each fraction group or individual file their sample in the queue page.


In this case, all the CPTAC files in project example 2 are fractions from the same sample (17) so they all have been assigned to the sample called 17. For the full CPTAC project, there would be samples 1-22.

Assign the Mulitplex labels

Once the reagents are added and the samples are assigned, one can configure what the individual labels represent in the sample.


First assign the project, then the sample, then the reagent. Once the reagent is assigned, the drop down boxes for Label should populate with the labels available for that reagent.

Assign each individual label for the reagent a phenotype. The phenotypes Control, Treatment, and Reference are currently supported (do not change these). Support for different phenotype assignments will happen in the future.

The identifier is generally related to the metadata for the study. In this case, 06CO002 (for example) represents a particular individual in the CPTAC study and Solid Tissue Normal represents the phenotype, but the exact format is not important, but they should be unique per project (i.e. do not reuse 06CO002 Solid Tissue Normal for another identifier in the same project.

Run the project

The multiplexed project should now have everything configured and should be able to be run like any other project. See Running Metaprod for more information.