A multiconsensus report is a result file generated from a workflow that includes the results of multiple processing steps. A multiconsensus report is not a merging of reports, but a reprocessing of the results.

The result report displays the combined results in columns that are labeled by search engine type, for example, Score Mascot and Score Sequest HT.

  • On the Proteins page, the columns #PSMs, # Peptides, Coverage, and Score display information side by side for each protein. When the proteins referenced in the individual searches have different accession numbers, the application displays the accession number of the first search in the result set.
  • On the PSMs page, the Search ID column displays the order in which the search was submitted to the job queue. A multiconsensus report resulting from a workflow that includes both Sequest HT and Mascot contains XCorr (Sequest HT) or Ions Score (Mascot) columns. These columns score the number of fragment ions that are common to two different peptides with the same precursor mass and calculate the cross-correlation score for all candidate peptides queried from the database. The default setting shows the top matches per peptide and search engine.

The identification information from the individual search nodes appears side by side on the PSMs page and the Peptide Groups pages. The grouped peptides represent the unified information from all matches found for this particular peptide sequence—not actual matches found during the search.

You can access the peptide information by examining:

  • The Proteins page for all peptides associated with a protein
  • The PSMs page for all peptides, including those not associated with a protein

You can view the associated peptides on the Proteins page. Select a protein row and select Show Associated Tables at the bottom of the page.

Special Processing Workflow Nodes and Node Settings

Include at least two search engine nodes, for example, Sequest HT and Mascot.

Workflow with multiple search engines
Workflow with multiple search engines

Special Consensus Workflow Nodes and Node Settings

The Merge Mode parameter of the MSF Files node determines how the application merges the data.

Setting the Merge Mode parameter of the MSF Files node

Globally by Search Engine Type Setting

The default setting of the Merge Mode parameter of the MSF Files node, Globally by Search Engine Type, merges the results of all search nodes of the same type. It displays the best PSM values on the Peptide Groups page and shows the combined protein score that was calculated from all PSMs identified by the search engine type.

The following figure displays the merged results of all Sequest HT and Mascot nodes and one protein score by node type on the Peptide Groups page.

The results from the two different search engine types appear together in two different column groups:

  • The top illustration shows them grouped on the Peptide Groups page.
  • The bottom illustration shows them grouped on the Proteins page.
Results grouped by search engine type on the Peptide Groups page and the Proteins page

Per File and Search Engine Type Setting

The Per File and Search Engine Type setting of the Merge Mode parameter of the MSF Files node merges the results of all search engine nodes of the same type for each input file.

In the following figure, the results report displays one group of search-engine-specific values per file and the search engine type. There are two groups of Sequest HT columns and two groups of Mascot columns. The top illustration shows the data grouped on the Peptide Groups page, and the bottom illustration shows it grouped on the Proteins page.

Results grouped by search engine type for each input file on the Peptide Groups page and the Proteins page

Do Not Merge Setting

The Do Not Merge setting of the Merge Mode parameter of the MSF Files node displays the search-engine-specific values for each search engine. (It does not merge nodes.) The File Limit for Automatic Merge parameter of the MSF Files Node sets an upper limit on the number of files that the report can display for unmerged data.

The following figure shows four groups of Sequest HT columns and two groups of Mascot columns. The top illustration shows the data grouped on the Peptide Groups page, and the bottom illustration shows it grouped on the Proteins page.

Results in one group of search-engine-specific values per search node on the Peptide Groups page and the Proteins page

Further Information

For more information on the MSF Files node, see the MSF Files node in the Proteome Discoverer Help.