As a default only the peaks currently annotated by a fragment ion is shown in the foreground. The other peaks are shown in grey in the background. Only (red) peaks in the foreground can be selected. To move all peaks to the foreground click the Show All Peaks option in the menu below the spectrum.
DeNovoGUI automatically annotates the a spectrum with the
most likely ions given the spectrum and the peptide sequence identified.
This includes the automatic selection of neutral losses.
However, the user can override the default annotation by selecting
different ion types in the menu below the spectrum. To change the neutral
losses one first has to uncheck the Adapt option on the Loss menu.
To make sure that the same ion types are used for all spectra, the user
can also turn of the automatic annotation completely in the Settings
menu.
Note that the spectrum annotation is relative to the sequenced peptide, even
if the de novo sequencing contains gaps at the terminals. In other words y1
is not always strictly speaking y1, but can be y1 + the mass of the gap. If
there is a gap it is annotated in peptide sequence by '...' as the terminal
at the respective terminal, and the mass of the gap is listed in the N-Gap
and C-Gap columns in the De Novo Peptides table.
Zooming is achieved by clicking and holding the left mouse button where you want to start the zoom, and then drag in the direction you want to zoom, marking the area to be zoomed. Right clicking in the plot undos the zoom.
In DeNovoGUI there are two ways of doing de novo sequencing: manual or automatic.
Manual: Click on one peak. The distance
and amino acids matching this distance (if any) will then
be shown. To add the sequence, click on the second peak.
Repeat the process to sequence more peaks.
An added sequence is removed by holding down the Ctrl button when clicking on
the sequence. To "store" a sequence, hold down the Alt button
and click on the sequence, the sequence turns red. To
remove such "stored" sequences, hold down Ctrl and Alt and
click in the sequence.
Automatic: Go to the De novo option in the menu below the
spectrum and select which ion type you would like to annotate. Note that
this annotation only tries to find matches against the sequence identified
by the PSM, and as such only gives an overview over the match between the
sequence and the spectrum for the selected ion types. For a complete de novo
sequencing showing all options for each distance use the manual option.
See also Annotation.