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This topic describes utilities for managing tandem mass spectrometry data. A folder of type MS2 displays the MS2 Dashboard as the default page for the folder providing an overview of the MS2 data stored there.

The default page includes some of the following web parts. You can add or remove any of these, or reposition them on the dashboard.

  • Data Pipeline: A list of jobs processed by the Data Processing 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.
  • MS2 Runs A list of processed and imported runs. Click on the description of a run to view it in detail, or look across runs using the comparison and export functionality. It also integrates experiment information.
  • Protein/Peptide Search: Provides a quick way to search for a protein or peptide identification in any of the runs in the current folder, or the current folder and all of its subfolders.
  • MS2 Sample Preparation Runs: A list of runs conducted to prepare the MS/MS sample.
  • Run Groups: A list of groups associated with MS2 runs. Click on a run group's name to view its details.
  • Run Types: A list of links to experiment runs by type.
  • Sample Types: A list of sample types present, if any.
  • Assay List: A list of assay designs defined in the folder or inherited from the project level.
  • Pipeline Protocols: A list of pipeline protocols present, if any.

MS2 Runs

The MS2 Runs web part displays a list of the runs in this folder. Click a run for more details. The following image shows this web part displaying sample data from the tutorial: Discovery Proteomics Tutorial

From this web part you can:

  • View, manage, and delete runs
  • Move runs to another folder
  • Add selected runs to groups
  • Compare peptide, protein, and ProteinProphet results across runs
  • Export data to other formats

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