Proteomics: MaxQuant workflow

proteomics-maxquant-label-free/maxquant-label-free

Author(s)

Version
8
Last updated
Nov 15, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Label-free data analysis using MaxQuant
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00157
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nProtein_database"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSample1"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nSample2"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["MaxQuant"];
  0 -->|output| 3;
  1 -->|output| 3;
  2 -->|output| 3;
  4["Filter"];
  3 -->|proteinGroups| 4;
  5["Select"];
  4 -->|out_file1| 5;
  6["Cut"];
  5 -->|out_file1| 6;
  7["Sort"];
  6 -->|out_file1| 7;
  8["Compute"];
  6 -->|out_file1| 8;
  9["Sort"];
  7 -->|outfile| 9;
  10["Compute"];
  8 -->|out_file1| 10;
  11["Cut"];
  10 -->|out_file1| 11;
  12["Compute"];
  10 -->|out_file1| 12;
  13["Histogram"];
  12 -->|out_file1| 13;

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
8 1a316efff 2020-11-15 23:35:58 update wf parameter
7 dffe67cc1 2020-10-31 19:54:12 Updating figure and workflow
6 3fd8e24d1 2020-10-22 11:42:53 Adding steps to workflow
5 cf8b1cb05 2020-08-31 01:11:11 Update some workflow names for consistency
4 cdab43efb 2020-08-03 04:07:53 update maxquant workflow histogram version to 1.0.4, add test
3 ba67a0dfe 2020-06-07 22:01:16 Adding a few more follow up steps and improving some older training content
2 5d041fcf7 2020-04-29 16:49:34 adding more stuff to the workflow
1 83de9bde8 2020-04-29 15:54:56 Adding MaxQuant training and levels for other proteomics tutorials

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.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