If more than one protein in a group has the same score, an equal number of PSMs, and an equal number of peptides, the protein with the longest sequence is designated as the master protein. The application marks master proteins with a green check mark in the Master column of the Proteins page of the result file.
Because the choice of a master protein can be arbitrary, the application also marks master protein candidates with a blue check mark. Master protein candidates are proteins that the application discarded as master proteins because of their shorter sequence. However, they are in the same protein group and have the same number of identified peptides as the master protein.
The application overlays the check marks of master protein candidates that it rejected with a gray “not” or “prohibited” sign, .
NOTE
If the consensus workflow includes the Display Settings node with the default filter settings, the Proteins page displays only master proteins at the top level by default when you open a result file.
The display at the top of the report is controlled by a factory filter set specified by the Default Filter Set parameter in the Administration view. To temporarily display a different set of proteins on this page, see Apply stored filters to a result file. For more information on filtering data, see Filtering results data.
Charts available on the Proteins page
To help you interpret your search results, you can generate the following charts on the Proteins page:
- Protein Identification Details view (see Use the Protein Identification Details view).
- Report Item Distribution chart (see Use the Report Item Distribution Charts).
- Sequence Comparison view (see Use the Sequence Comparison view).
- Enrichment Chart View (see Display the Enrichment Chart).
- Biochemical Pathway Map (see Use Pathway Maps).
- Quan Ratio Distributions (see Display Quantification Ratio Distribution charts).
- Trend Chart (see Display the Trend Chart).
- Quan Channel Values chart (see Display the Quantification Channel Values chart).