MaxQuant MSstatsTMT Training

proteomics-maxquant-msstats-tmt/main-workflow

Author(s)

Version
1
Last updated
Aug 13, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
MaxQuant and MSstats for the analysis of TMT data
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00159
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nInput Dataset Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nExperimental design template"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nMSstats annotation file"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["MaxQuant"];
  0 -->|output| 3;
  1 -->|output| 3;
  4["MSstatsTMT"];
  2 -->|output| 4;
  3 -->|evidence| 4;
  3 -->|proteinGroups| 4;

Inputs

Input Label
Input dataset collection Input Dataset Collection
Input dataset Experimental design template
Input dataset MSstats annotation file

Outputs

From Output Label
Input dataset collection Input Dataset Collection
Input dataset Experimental design template
Input dataset MSstats annotation file
toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2 MaxQuant
toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0 MSstatsTMT

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 8926310c6 2021-08-13 14:05:50 correcting workflow
1 0d66511e2 2021-08-13 13:59:08 new maxquant msstats tmt training

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-tmt/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows