Proteomics: MaxQuant and MSstats LFQ workflow
proteomics-maxquant-msstats-dda-lfq/main-workflow
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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
Input | Label |
---|---|
Input dataset | annotation file |
Input dataset | comparison matrix |
Input dataset | fasta protein database |
Input dataset collection | raw files |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4 | MaxQuant | |
Grep1 | Select | |
Grep1 | Select | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 | Replace Text | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 | Replace Text | |
toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1 | MSstats | |
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6 | Datamash | |
Summary_Statistics1 | Summary Statistics | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 | Replace Text | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 | Replace Text | |
Filter1 | Filter | |
Filter1 | Filter | |
Filter1 | Filter | |
Filter1 | Filter | |
Filter1 | Filter | |
Cut1 | Cut | |
Cut1 | Cut | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | Join | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | Join | |
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1 | heatmap2 | |
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2 | UniProt | |
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1 | heatmap2 | |
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2 | UniProt | |
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 | FASTA-to-Tabular | |
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 | FASTA-to-Tabular |
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
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 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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
3 | e1daddc51 | 2021-06-04 05:26:15 | fixing broken boxes, adjusting results for actual set MSstats parameters |
2 | 0463f30a6 | 2021-06-03 12:22:34 | changed Maxquant parameters and removed middle part of training |
1 | ae8154eef | 2021-02-17 11:59:25 | Adding new maxquant msstats tutorial |
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