metaproteomics

Metaproteomics

Files

Workflow: metaproteomics.ga

History file: Sample_Peptide_Shaker_PSM_Report.tabular

Required Galaxy Tools

If you wish to run the metaproteomics workflow on your own Galaxy instance you will need to install the following, versioned, tools:

Tool Name	Owner	Version
fasta_compute_length	devteam	de2db1bdfbf8
fasta_filter_by_length	devteam	2fd6033d0e9c
fasta_to_tabular	devteam	7e801ab2b70e
query_tabular	iuc	1ea4e668bf73
tabular_to_fasta	devteam	0b4e36026794
text_processing	bgruening	6378f8384f30

Workflow Instructions

The example metaproteomics workflow using Query Tabular has been implemented within the same accessible instance as described above for the proteogenomics examples. - To access this example workflow, follow these steps:

1. Go to https://z.umn.edu/metaproteomicsgateway. To utilize this instance, you must be registered and logged in. Follow the instructions above for the proteogenomics example above to do this.

2. Once registered, workflows and sample input data can be accessed within the Shared Data tab.

   • To run the workflow, first appropriate input data must be loaded into your active History. Clickon Shared data and select Histories. From the list of shared Histories, select QueryTabular_input_F1000. In the page that appears, select Import History and click on Import when the window appears.
   • Next click on Shared Data, select Workflows
   • When the shared Published Workflows page appears, type Query in the search field
   • The workflow titled Query Tabular F1000 Metaproteomics: PSM Report to Blast Input Peptides will come up. Click on the drop down arrow on the right of the workflow button, and select Import
   • In the green box that appears, click on Start using this workflow.
   • This will now show up in Your workflows. Click on the dropdown arrow and select Run.
   • The next window will show the steps in the workflow. The first item shows the input data that you just imported into your History that will be processed by the workflow (Sample_Peptide_Shaker_PSM_Report.tabular)
   • Click on Run workflow and the analysis will proceed.