The protein window displays a list of the proteins identified in your sample.
This window appears automatically once a search has completed, or when you press the PROTEIN button from the toolbutton window.
In the above figure, we see the proteins identified from a MS/MS dataset.
A: With a MassAI score of 16000+, calreticulin is by far the most abundant protein in the sample.
B: This window shows the peptide coverage of the protein currently selected in window A.
C: This list contains information on the individual peptides identified for selected protein.
When you select a peptide from here, the sequence is highlighted in window B (blue colour), and all related scans are listed in window
D: Scans representing the currently selected peptide. Scans of any quality are listed here. The ones with a score above cutoff are listed
in green, scans below cutoff are in yellow.
E: This window lists all proteins in which the selected peptide has been observed. In this case, the peptide sequence
IKDPDASKEDWDER is present only in Calreticulin within the search space - which is the human proteome.
When you select a scan in window D, the
corresponding, annotated scan is shown in a
From this window you can trim down your protein results, keep the ones thst you want
and export sequences into text files, FASTA format.