In previous versions of the Proteome Discoverer application, you could only open the .pdResult file produced by the Consensus workflow to see the list of protein and peptide identifications for a given analysis. In the Proteome Discoverer 3.1 application, you can now view the contents of an MSF file.
The MSF file contains the information that the Processing workflow produces, most notably the MS/MS Spectrum Info table, the PSMs table, and the Proteins table.
NOTE
The following figure does not show the Peptide Groups table, which the PSM Grouper node usually creates in the Consensus workflow.
The following figure is an example of a standard MSF file.
Because it is recommended to only use a Processing workflow to run large studies with automation, you can create the Peptide Groups table by using the new PSM and Protein Grouper node found in the Post-Processing nodes section. The PSM and Protein Grouper node does the following:
- Creates the Peptide Groups table
- Calculates the FDR for Peptide Groups and Proteins
- Adds additional columns for FDR measurement to the Proteins table
- Filters the q-value with a threshold of 0.01
The PSM and Protein Grouper node lets you calculate the number of proteins and peptides that are identified in a dataset without having to produce a .pdResult file.
The following figure shows the results from the same dataset with the addition of the PSM and Protein Grouper node in the Processing workflow.