By default the results report (.pdResult file) opens to the Proteins page.

Figure Commonly used columns on the Proteins page

The Proteins page reports all of the proteins identified in the experiment that pass any user-defined threshold such as FDR. From this page, you can see the UniProt Accession and the number of proteoforms and isoforms of each protein identified in the experiment. Additionally, the number of PrSMs and characterized proteoforms (that is, proteoforms with C-Score greater than 40) are listed. If you enabled FDR, then the Q-Value for each protein is also displayed.

You can access additional information for each protein identified by selecting it and selecting the down arrow next to Show Associated Tables, .
Table Commonly used columns on the Proteins page

Column

Description

Accession

UniProtâ„¢ accession identifiers used to cite UniProt entries.

# of Isoforms

The number of isoforms identified from the associated protein accession.

# of Isoforms with Characterized Proteoforms

The number of isoforms with proteoforms that have a C-Score greater than 40.

# Proteoforms

The number of identified proteoforms from the associated UniProt protein accession.

Proteoform Characterization Confidence

The visual indication of C-Score confidence (default values are >40=green,<40->3=yellow, <3=red). You can define these thresholds in the ProSight Protein and Proteoform Filter node in the consensus workflow.

# Characterized Proteoforms

The number of proteoforms having a C-Score greater than 40.

Q-value

The likelihood of discovering the associated protein by chance given the experimental evidence.

Localized Modifications

Proteoform post-translational modifications confidently localized by fragment matches in one or more PrSMs.

Non-localized Modifications

Proteoform post-translational modifications that could be confidently localized by fragment matches in any PrSM.