The MS2 run detail page shows data from a single run.

Run Overview

The run overview provides metadata about the run and how the search was performed. This information is derived from the pepXML file associated with the run. Or for COMET searches, this metadata comes from a comet.def (definitions) file within the tar.gz file.

Information shown includes:

  • Search Enzyme: The enzyme applied to the protein sequences by the search tool when searching for possible peptide matches (not necessarily the enzyme used to digest the sample).
  • Search Engine: The search tool used to make peptide and protein matches.
  • Mass Spec Type: The type of MS instrument used to analyze the sample.
  • Quantitation: The source of quantitation algorithms used.
  • File Name: The name of the file where the search results are stored.
  • Path: The location of the file named above.
  • FASTA File: The name and location of the copy of the protein sequence database searched.
Links here let you:
  • rename the run
  • show protein modifications
  • show the tandem.xml search protocol definition file used by the search engine
  • show peptide or protein prophet details

View

Ways of grouping and filtering your results can be saved as a named 'view' of the data, which can later be applied to other similar datasets. Select among existing saved views and click Go or create and save your own.

Use the options in the View section, or make grid based changes in the Peptides and Proteins section.

Grouping

Options for grouping the Peptides and Proteins grid include:

  • Standard lists all the peptides from the run. See additional filters below.
  • Protein Groups shows information from the ProteinProphet groups.
  • Peptides (Legacy) lists all the peptides from the run and the corresponding columns of peptide information without nesting them.
  • Protein (Legacy) displays a summary of the protein matches from the run, as assigned by the search engine, and the corresponding columns of protein information.
  • ProteinProphet (Legacy) displays a summary the results of the ProteinProphet analysis, including a confidence score that the protein has been identified correctly.
If you select the Expanded checkbox the data will all be expanded by default to show components.

To add or remove columns for any grouping, select Grid Views > Customize Grid. Some columns may nest under others in the grid.

View Filters

There are special filters available in the View section that offer specialized features not available in typical grid filtering. Not all options are available in all Groupings of data.

  • Hyper charge filter allows you to filter by charge, select the minimum Hyper value for peptides in charge states 1+, 2+ and 3+, then click Go.
  • Minimum tryptic ends specifies how many ends of the peptide are required to match a tryptic pattern: 0 means all peptides will be displayed; 1 means the peptide must have at least one tryptic end; and 2 means both ends must be tryptic.
  • Highest score filter allows you to filter out all except the highest Hyper score for a peptide.
  • RawScore filter offered for the COMET search engine specifies different raw score thresholds for each charge state. For example, if you enter 200, 300, and 400 in these three text boxes, you are specifying 1+ peptides with raw scores greater than 200, 2+ peptides with raw scores greater than 300, and 3+ peptides with raw scores greater than 400.

Saving Views

You can save a specific combination of grouping, filtering parameters, column layout, and sorting as a named view. Click Save View to do so. Later selecting that saved view from the menu will apply those same parameters to other runs or groups of runs. This makes it easier to keep your analysis consistent across different datasets.

Manage Views

To delete an existing view, select a default, or indicate whether you want to use the current view the next time you look at another MS2 run, click Manage Views.

Peptides and Proteins Section

The Peptides/Proteins section displays the peptides and/or proteins from the run according to the sorting, filtering, and grouping options you select.

You can customize the display and layout of the Peptides/Proteins section, as with other data grids:

  • Choose which columns of information are displayed, and in what order, by selecting Grid Views > Customize Grid. See Peptide Columns and Protein Columns for more information.
  • Sort the grid, including sorting by multiple columns at once.
  • Filter the grid using the column header menu option Filter.
Note: Only the first 1,000 scans (in the case of no grouping) or 250 proteins (for the Protein Collapsed or Expanded groupings) are displayed. To display scans or proteins not shown in this list, adjust your filter to return fewer results. For example, you can filter on a range of scan numbers or a range of protein names to return a particular subset of results.

Getting More Detail

Some of the fields in the rows of peptide and protein data are links to more detailed information.

  • Click the Scan number or the Peptide name to go to the Peptide Spectrum page, which displays the MS2 spectrum of the fragmented peptide.
  • Click the Protein name to go to the Protein Details page, which displays information on that protein and the peptides from the run that matched it.
  • Click the dbHits number to go to the Protein Hits page, which displays information on all the proteins from the database that the peptide matched.
Exporting

You can export data from the MS2 Peptides/Proteins page to several other file types for further analysis and collaboration. Before you export, make sure the grid you have applied includes the data you want to export.

For more information on exporting MS2 data, see Export MS2 Runs.

Viewing a GO Piechart

For any run, you can display a GO Piechart by clicking on the "Gene Ontology Charts" button above the peptides list. Select the desired chart type (Cellular Location, Molecular Function or Metabolic Process) from the drop-down menu.

For example, this GO Cellular Location Chart is available in the the Proteomics Demo. Clicking a wedge will present details about that pieslice.

Discussion

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