Proteomics: MaxQuant and MSstats LFQ workflow

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Australia
• Galaxy France
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nannotation file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncomparison matrix"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nfasta protein database"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Collection\nraw files"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["MaxQuant"];
  2 -->|output| 4;
  3 -->|output| 4;
  5["Select"];
  4 -->|proteinGroups| 5;
  6["Select"];
  4 -->|evidence| 6;
  7["Replace Text"];
  5 -->|out_file1| 7;
  8["Replace Text"];
  6 -->|out_file1| 8;
  9["MSstats"];
  1 -->|output| 9;
  0 -->|output| 9;
  8 -->|outfile| 9;
  7 -->|outfile| 9;
  10["Datamash"];
  9 -->|runlevel_data| 10;
  11["Summary Statistics"];
  9 -->|runlevel_data| 11;
  12["Replace Text"];
  9 -->|comparison_result| 12;
  13["Replace Text"];
  9 -->|quant_sample_matrix| 13;
  14["Filter"];
  12 -->|outfile| 14;
  15["Filter"];
  14 -->|out_file1| 15;
  16["Filter"];
  14 -->|out_file1| 16;
  17["Filter"];
  15 -->|out_file1| 17;
  18["Filter"];
  16 -->|out_file1| 18;
  19["Cut"];
  17 -->|out_file1| 19;
  20["Cut"];
  18 -->|out_file1| 20;
  21["Join"];
  13 -->|outfile| 21;
  19 -->|out_file1| 21;
  22["Join"];
  13 -->|outfile| 22;
  20 -->|out_file1| 22;
  23["heatmap2"];
  21 -->|output| 23;
  24["UniProt"];
  21 -->|output| 24;
  25["heatmap2"];
  22 -->|output| 25;
  26["UniProt"];
  22 -->|output| 26;
  27["FASTA-to-Tabular"];
  24 -->|outfile_retrieve_fasta| 27;
  28["FASTA-to-Tabular"];
  26 -->|outfile_retrieve_fasta| 28;

Inputs

Outputs

Tools

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

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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/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