The Proteoforms page displays all of the identified proteoforms.

Figure The Proteoforms page

The Proteoforms page also includes the identified sequence for each proteoform and the number of supporting PrSMs, theoretical mass in kDa, search engine confidence, -Log P-Score, -Log E-Value, best PrSM C-score, and Sequence Coverage (as % residue cleavage.) If FDR is enabled, proteoform level Q-Values are also displayed.

For each result at the proteoform level, you can launch the ProSight Lite and TDValidator Lite applications. For additional information on these applications, see the following topics:

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

Column

Description

Proteoform Characterization Confidence

Visual indication of C-Score confidence (>40=green, <40->3=yellow, <3=red). For information on defining the parameters, see PrSM Grouper node.

Sequence

Proteoform sequence.

# PrSMs

Number of proteoforms.

Theo Mass [Da]

Proteoform mass based on the matched sequence.

Confidence

Visual representation of the proteoform’s PrSM confidence based on the -log E-value levels specified in the ProSightPD configuration.

Higher confidence = green, medium confidence = yellow, and low confidence = red

-Log P-Score

Statistical confidence for proteoform assignment. Large positive numbers are more confident. Values less than 4 are considered poor.

-Log E-Value

Statistical confidence for proteoform assignment adjusted for the search space.

Best PrSM C-Score

Highest C-Score of PrSMs supporting the associated proteoform.

Average PrSM Detected Neutral Mass

Average observed mass from all PrSMs associated with a proteoform.

% Residue Cleavages

Percentage of observed fragments compared to the total possible cleavages. Also known as sequence coverage.

External Top Down Displays

Select to view the result in the ProSight Lite or the TDValidator Lite applications. For more information, see Use ProSight Lite and Use TDValidator Lite.

Proforma

The proforma sequence notation for the proteoform identification.