Proteomics: MaxQuant and MSstats for the analysis of label-free data

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nProtein Groups"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nEvidence"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nannotation file"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\ncomparison matrix"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Select"];
  0 -->|output| 4;
  58469745-c560-4082-9cc4-2a457386b772["Output\nselect protein groups"];
  4 --> 58469745-c560-4082-9cc4-2a457386b772;
  style 58469745-c560-4082-9cc4-2a457386b772 stroke:#2c3143,stroke-width:4px;
  5["Select"];
  1 -->|output| 5;
  cfff2740-c583-4e2d-bf6d-2dc5ecbb69f5["Output\nselect protein evidence"];
  5 --> cfff2740-c583-4e2d-bf6d-2dc5ecbb69f5;
  style cfff2740-c583-4e2d-bf6d-2dc5ecbb69f5 stroke:#2c3143,stroke-width:4px;
  6["Replace Text"];
  4 -->|out_file1| 6;
  aa963300-6a11-4455-a0e2-17cb68483426["Output\nprotein groups input for MSstats"];
  6 --> aa963300-6a11-4455-a0e2-17cb68483426;
  style aa963300-6a11-4455-a0e2-17cb68483426 stroke:#2c3143,stroke-width:4px;
  7["Replace Text"];
  5 -->|out_file1| 7;
  b746188c-8a93-4d78-9379-2ed054a136d2["Output\nevidence input for MSstats"];
  7 --> b746188c-8a93-4d78-9379-2ed054a136d2;
  style b746188c-8a93-4d78-9379-2ed054a136d2 stroke:#2c3143,stroke-width:4px;
  8["MSstats"];
  3 -->|output| 8;
  2 -->|output| 8;
  7 -->|outfile| 8;
  6 -->|outfile| 8;
  9["Summary Statistics"];
  8 -->|proteinlevel_data| 9;
  10["Replace Text"];
  8 -->|quant_sample_matrix| 10;
  9dff3f51-ec15-4737-ac31-4af0bbce163e["Output\nreplaced sample quantification matrix"];
  10 --> 9dff3f51-ec15-4737-ac31-4af0bbce163e;
  style 9dff3f51-ec15-4737-ac31-4af0bbce163e stroke:#2c3143,stroke-width:4px;
  11["Replace Text"];
  8 -->|comparison_result| 11;
  c69337e8-a296-4b01-b439-e41d7a397099["Output\nreplaced comparison result"];
  11 --> c69337e8-a296-4b01-b439-e41d7a397099;
  style c69337e8-a296-4b01-b439-e41d7a397099 stroke:#2c3143,stroke-width:4px;
  12["Datamash"];
  8 -->|proteinlevel_data| 12;
  13["Filter"];
  11 -->|outfile| 13;
  ef566712-0057-4d2e-8b66-fca422b71031["Output\nsignificant proteins"];
  13 --> ef566712-0057-4d2e-8b66-fca422b71031;
  style ef566712-0057-4d2e-8b66-fca422b71031 stroke:#2c3143,stroke-width:4px;
  14["Filter"];
  13 -->|out_file1| 14;
  81583c93-be46-4b0a-8b8f-43f1c700c900["Output\nmetastasized filtered"];
  14 --> 81583c93-be46-4b0a-8b8f-43f1c700c900;
  style 81583c93-be46-4b0a-8b8f-43f1c700c900 stroke:#2c3143,stroke-width:4px;
  15["Filter"];
  13 -->|out_file1| 15;
  dfe7380c-7b63-4381-84d4-08f225a165c6["Output\nrdeb filtered"];
  15 --> dfe7380c-7b63-4381-84d4-08f225a165c6;
  style dfe7380c-7b63-4381-84d4-08f225a165c6 stroke:#2c3143,stroke-width:4px;
  16["Filter"];
  14 -->|out_file1| 16;
  a83ef0a1-d7b6-43b2-be66-394e6b5af4b0["Output\nsignificant metastasized"];
  16 --> a83ef0a1-d7b6-43b2-be66-394e6b5af4b0;
  style a83ef0a1-d7b6-43b2-be66-394e6b5af4b0 stroke:#2c3143,stroke-width:4px;
  17["Filter"];
  15 -->|out_file1| 17;
  bbafbb4f-7d4a-43aa-9a47-078f5c946ff5["Output\nsignificant rdeb"];
  17 --> bbafbb4f-7d4a-43aa-9a47-078f5c946ff5;
  style bbafbb4f-7d4a-43aa-9a47-078f5c946ff5 stroke:#2c3143,stroke-width:4px;
  18["Cut"];
  16 -->|out_file1| 18;
  4b9eed6a-3316-41e8-ad1a-f6252bca9888["Output\nmetastasized cut"];
  18 --> 4b9eed6a-3316-41e8-ad1a-f6252bca9888;
  style 4b9eed6a-3316-41e8-ad1a-f6252bca9888 stroke:#2c3143,stroke-width:4px;
  19["Cut"];
  17 -->|out_file1| 19;
  4a99a360-9afc-4358-bed1-ed3a10aa1310["Output\nrdeb cut"];
  19 --> 4a99a360-9afc-4358-bed1-ed3a10aa1310;
  style 4a99a360-9afc-4358-bed1-ed3a10aa1310 stroke:#2c3143,stroke-width:4px;
  20["Join"];
  10 -->|outfile| 20;
  18 -->|out_file1| 20;
  f5759e17-57b3-4ca7-b09a-172fdcc0aa21["Output\nmetastasized join"];
  20 --> f5759e17-57b3-4ca7-b09a-172fdcc0aa21;
  style f5759e17-57b3-4ca7-b09a-172fdcc0aa21 stroke:#2c3143,stroke-width:4px;
  21["Join"];
  10 -->|outfile| 21;
  19 -->|out_file1| 21;
  f8de348d-f22c-47e9-8899-40e525c51966["Output\nrdeb join"];
  21 --> f8de348d-f22c-47e9-8899-40e525c51966;
  style f8de348d-f22c-47e9-8899-40e525c51966 stroke:#2c3143,stroke-width:4px;
  22["UniProt"];
  20 -->|output| 22;
  0a40e034-7710-4a02-9950-98baa4b4a7cf["Output\nmetastasized uniprot"];
  22 --> 0a40e034-7710-4a02-9950-98baa4b4a7cf;
  style 0a40e034-7710-4a02-9950-98baa4b4a7cf stroke:#2c3143,stroke-width:4px;
  23["heatmap2"];
  20 -->|output| 23;
  02709f6c-fffe-416e-a76d-ff03c1eb5bc4["Output\nUpregulated proteins in metastasized cSCC"];
  23 --> 02709f6c-fffe-416e-a76d-ff03c1eb5bc4;
  style 02709f6c-fffe-416e-a76d-ff03c1eb5bc4 stroke:#2c3143,stroke-width:4px;
  24["heatmap2"];
  21 -->|output| 24;
  690b708f-52d6-4caf-b20f-2a464fbd798e["Output\nUpregulated proteins in RDEB cSCC"];
  24 --> 690b708f-52d6-4caf-b20f-2a464fbd798e;
  style 690b708f-52d6-4caf-b20f-2a464fbd798e stroke:#2c3143,stroke-width:4px;
  25["UniProt"];
  21 -->|output| 25;
  33419abf-0efa-4a28-8cab-d28f645ea2c3["Output\nrdeb uniprot"];
  25 --> 33419abf-0efa-4a28-8cab-d28f645ea2c3;
  style 33419abf-0efa-4a28-8cab-d28f645ea2c3 stroke:#2c3143,stroke-width:4px;
  26["FASTA-to-Tabular"];
  22 -->|outfile_retrieve_fasta| 26;
  27["FASTA-to-Tabular"];
  25 -->|outfile_retrieve_fasta| 27;

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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