You can display the complete sequences for different proteins with the Sequence Comparison view. You can use this feature to compare similar proteins that share varying degrees of identical peptide sequences or to compare the complete sequences of different proteins associated with a single peptide.
Procedure
- In an open report, click the Proteins tab.
- Highlight the rows of the proteins that you want to compare.
- Choose View > Sequence Comparison, or click the Sequence Comparison icon,
. - The Sequence Comparison view opens.
Sequence Comparison view
The sequence table shows the complete amino acid sequence of the currently selected protein files. The portions of the sequence that match the searched sequence are highlighted in a color that represents the confidence in the identification:
- Green: Highlighted peptides of high confidence
- Yellow: Highlighted peptides of medium confidence
- Red: Highlighted peptides of low confidence
The application highlights in blue any letters in an amino acid sequence that do not match the sequence that it compares them to.
The light blue column to the left of the table displays the accession numbers of the highlighted protein sequences being compared. The numbers in the dark blue column to the left of the sequence table and the numbers in the dark blue header on top of the sequence table help you find automatically assigned amino acid numbers in the table. The numbers in the left column are displayed in increments of 100, and the numbers on top of the table are displayed in increments of 10.
You can select peptide groups or PSMs in the associated tables of the selected protein. The application then underlines the sequences in the sequence table of the selected peptides.