PeptideShaker 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 this dialog or in the menu below the spectrum. Note that to change the neutral
losses in the menu below the spectrum 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 by unchecking the
Automatic Annotation option.
The high resolution option optimizes the spectrum annotation for high resolution instruments,
by selecting the most accurate peak for annotation if there is more than one option.
For low resolution instruments this option should be deselected, resulting in that the
most intense peak is annotated if there is more than one option.
In addition to deciding which ion types to use when annotating the spectrum, the
user can also change the required accuracy of the annotations. This is done using
by using the scroll while while holding down the Ctrl key or by changing
the Fragment Ion Accuracy value in this dialog. Changing this value will
decrease or increase the accuracy required to say that a given peak
should be annotated. The maximum value is set to the fragment ion accuracy set
in the Search Parameters tab (found on the Edit menu).
Scrolling without holding down the Ctrl key
(or editing the Annotation Level value in this dialog)
lets the user decide how many of the peaks PeptideShaker should try to annotate.
The level is set relative to the most intense peak, e.g., 80% means that only
peaks with an intensity that is at least 80% of the most intense peak are considered. As
the value is reduced, more and more of the low intensity peaks will be annotated.
The annotation colors plus the width and color of the peaks can be edited from the Settings menu below the spectrum, choose Settings > Annotation Colors.