A folder of type MS2 displays the MS2 Dashboard as the default page for the folder. The MS2 Dashboard shows an overview of the MS2 data stored in the current folder.

This overview displays the following information. You can remove any of these web parts, or reposition them on the dashboard.

• MS2 Runs: A simple list of runs that have been processed and analyzed by CPAS. Click on the description of a run to view it in detail.
• MS2 Runs (Enhanced): A list of processed runs that offers advanced features, including comparison of run data and export functionality. It also integrates experiment information.
• MS2 Sample Preparation Runs: A list of runs conducted to prepare the MS/MS sample.
• Data Pipeline: A list of jobs processed by the data Data Pipeline, including currently running jobs; jobs that have terminated in error; and all successful and unsuccessful jobs that have been run for this folder. Click on a pipeline job for more information about the job.
• Experiment Navigator: A list of experiments associated with MS2 runs. Click on an experiment name to view details about the experiment.

If you are working in a folder of type Custom rather than one of type MS2, you can customize the folder's Portal page to display whichever web parts you prefer. See Projects and Folders for more information about folder types.

MS2 Runs (Enhanced)

The MS2 Runs (Enhanced) web part displays detailed information about the runs in this folder. The following image shows this web part displaying sample data from the CPAS getting started tutorial.

Here you can:

• Manage, move, and delete runs
• Add selected runs to an experiment, and view experiment details
• Compare peptide, protein, and ProteinProphet results across runs
• Export data to other formats

Protein Search

As of CPAS version 2.0, you can search within the current folder and all of its subfolders for MS2 runs that have identified a particular protein.

To use this feature, add the Protein Search web part to the MS2 Dashboard page (or the Portal page). You must have administrative privileges on the folder in order to add the wb part.

To search for a protein, type in its name. If you have loaded protein annotations, you can also search for annotation values, like associated gene names. You can search for multiple proteins at once by entering the names separated by commas.

The top of the results page will show all the proteins that match your search and are part of a FASTA file referenced by one of the MS2 runs in the folder or its subfolders. Additionally, the page will show all of the protein groups identified by ProteinProphet that contain those proteins. You can modify the error rate or probability thresholds for those values.

By default, the search will look in the current folder and all of its subfolders, and will find only protein names or annotations that match your search exactly. You can modify these settings.

You can also add or remove columns from the results by clicking the customize view command.