The Runs table

The Runs table displays the run name, the upload date, the file size, the number of tandem mass spectra in the file and the number of sequence tags in the file. The original run data file, the spectra file (in MGF format) and the sequence tags file may be downloaded using the download links, .

Click the Public Runs button to list shared runs or the My +Public button to list your runs and shared runs.

Use the Filter field to filter the table list by run name or project name.

Use the view results link to see the results from all of the search outputs combined into a single result for that run.

Use the download link in the runs column, , to download the original data file. Large data files are archived after a set time and you may request retrieval of the file. Retrieval takes several days. The retrieved file will remain available for one week for download.

Click the run name to go to a page listing all searches for that run.

Use the edit metadata link, , to edit metadata fields such as sample name and to add comments about the run.

The Search Launcher

Use the New Search interface to start a search. Select the runs of interest using the checkbox fields in the runs table, then define the search settings.

Filter parameters by species (optional)
To filter down a large number of search parameter options, select the organism of interest.

Search parameters
Select the radio button and then select the desired search parameters in the pull-down list to search the selected runs using that search setting.

Workflows
Select the radio button and then select the desired workflow in the pull-down menu list to search the selected runs using that workflow setting. This will search the selected runs against all of the search parameters defined in the workflow.

N of nodes
Define the number of nodes in the compute cluster. One is generally sufficient.

Run searches: serial or parallel
Select serial to run all of the searches sequentially on a single compute cluster. Select parallel to run all of the searches on separate compute clusters in parallel.

Search Separately
Click this button to start the search, searching each run separately and generating separate outputs. This is the most common use case.

Merge & Search
Click this button to start the search, combining all of the runs into a single search input and generating a single output. This can be useful for MuDPIT-style experiments.

Launch experiment
Functionality is pending.

Add to project
Click to add the selected runs to an existing or new project. Runs may belong to multiple projects.

Delete
Click to delete the selected runs. CAUTION! This cannot be undone - deleted runs cannot be recovered.