Proteogenomics 2: Database Search
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This workflows is part of the tutorial Proteogenomics 2: Database Search, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Romane Libouban
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar, Delphine Lariviere
Tutorial Contributor(s): Saskia Hiltemann, Subina Mehta, Nicola Soranzo, Björn Grüning, Helena Rasche, Melanie Föll
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| MGF Collection | MGF Collection | n/a |
|
| Reference Protein Accessions | Reference Protein Accessions | n/a |
|
| Uniprot_cRAP_SAV_indel_translatedbed.FASTA | Uniprot_cRAP_SAV_indel_translatedbed.FASTA | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Identification Parameters | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1 |
| 4 | Search GUI | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy2 |
| 5 | Peptide Shaker | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy2 |
| 6 | mz to sqlite | toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.1.1+galaxy0 |
| 7 | Removing reference proteins | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
| 8 | Selecting sequence with length >6 and <30 | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
| 9 | Peptides_for_BlastP_analysis | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Search GUI on input dataset(s) | Search GUI on input dataset(s) | n/a |
|
| Mz to sqlite | Mz to sqlite | n/a |
|
| Removing reference proteins | Removing reference proteins | n/a |
|
| Selecting sequence with length >6 and <30 | Selecting sequence with length >6 and <30 | n/a |
|
| Peptides_for_BlastP_analysis | Peptides_for_BlastP_analysis | n/a |
|
Version History
master
8.0
Creators and Submitter
Views: 2518 Downloads: 334 Runs: 0
Created: 2nd Jun 2025 at 10:52
Last updated: 27th Apr 2026 at 14:55
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